Do any modern ("free-thinking") monks or monastic orders discard elements of the Vinaya?

I couldn't help but think that some of the rules were shockingly superstitious even by the standards of most of the world religions of the time. For example, rules that emphasize non-violence to such an extent that they forbid monks and nuns from slicing or peeling their own fruits and vegetables.

Just historically perhaps that is a middle (i.e. less extreme) way, compared to the doctrine of the Jains, which had started one generation before.

Is it permissible for a Buddhist lay follower, one who has taken refuge and has chosen to follow the Eightfold Path without picking and choosing, to discuss certain aspects of the vinaya in a skeptical light, as I have just done?

Well I think you have asked politely enough for this site, anyway. :-)

I'm mindful of this line from the Maha-parinibbana Sutta: Last Days of the Buddha (DN 16)

"If it is desired, Ananda, the Sangha may, when I am gone, abolish the lesser and minor rules.

The footnote there says,

Since Ananda, at this point, did not ask what the minor rules were, the Sangha decided not to abolish any of the rules of the Vinaya.

Apparently they didn't agree that some were "minor" and/or which were minor and, out of respect, kept them all as-is.

Within a school I think that the Vinaya famously doesn't change -- it's part of what defines "a tradition", for example "Theravada". So much so that there's even something, I forget what, which existing monks may do when they go to a new monastery, in case the rules at their previous monastery hadn't been followed correctly -- and so they take on the rules afresh, just to be sure -- conversely some might, even rightly, not trust the compliance-with-the-rules of other places/groups.

Comparatively:

• Japan might be exceptional or extreme in the non-standardness of its Vinaya -- where senior monks are allowed to marry. That might be because there was at least one episode in Japanese history where Buddhism was forcibly altered by the state.

• The Tibetan Vinaya is not unlike the Theravada -- it might be a superset? -- it too includes rules about "seeds of a plant" for example.

• I don't know about (non-Japanese) Zen, generally. I get the impression that the discipline in Plum Village (is that traditional Vietnamese I don't know) seems joyous for and welcoming of nuns, but who knows -- other nuns with any online presence that I've noticed might be joyful albeit experiencing some difficulties too, maybe it's something to "see for yourself".

Now in practice and not just in theory:

• If you read something like The Broken Buddha you can see there are some monks and monasteries who flout the rules, perhaps openly or perhaps hypocritically (monks don't necessarily welcome that book having been published as some might interpret it as bringing the whole Sangha into disrepute and/or harming the faith of laypeople).

• Sometimes there are controversies like bhikkhuni ordination for example.

I have not taken refuge in the Three Jewels and will not unless I can do so in total sincerity and a pure conscience.

It might help to understand that Sangha has at least two distinct meanings:

1. The groups of all presently-ordained people, monks and nuns
2. The "noble" sangha is the group of all present and past enlightened and semi-enlightened people -- including for example "Sotāpanna", monastic and/or lay

Conversely one of the monastic rules forbids monks from claiming attainment in front of laypeople -- in case laypeople will prefer (to gives alms to) the more enlightened, leaving others with no support.

Perhaps it's our duty, as people in general and even as laypeople, to be careful about what teaching and teachers we accept.

But I suspect that we shouldn't be too critical of the Sangha in general nor of (venerable) members of the sangha in particular, even if one were to believe that one might have seen some fault.

"Pure conscience" might mean that it's not an unvirtuous or unskilful action on your part, i.e. not something you regret or have remorse for.

Householder, it is good to take not refuge into fools.

Sn 1.5: Cunda Sutta — To Cunda

And obliviously, like most, you also already got corrupted by "modern and smart" monks of the last kind.

Of course one is free to join one or another alternative rebel group of thieves, like here, and share the ways of corruption with each other.

A "free thinking" monk isn't a monk but a fool, isn't even a disciple, since he/she hasn't gone to refuge obiviously but runs his ego-trip for gains and honor under monks and householder. So their follower are...

A wise thinking monks takes even the smallest rule more serious and reflects it's meaning also in other areas then it that of the stories and tends to how to make no mistake rather then usual "how to gain what I like in using ways around".

f looking for the "headquarter of missleaders" and thieves, just go to https://discourse.suttacentral.net/ and find all what a lost wishes to gain for his further lose.

(Note that this isn't given for stacks, exchange, trade... but "just" for escape from this corrupt wheel)

In accordance with the discipline a bhikkhu is prohibited from eating fruit or vegetables containing fertile seeds. So when offering such things, a lay person can either remove the seeds, or make the fruit allowable by slightly damaging it with a knife. This is done by piercing the fruit and saying at the same time "kappiya.m bhante" (meaning "I make this allowable, sir.").

There is a rule for monks to not damage fertile seeds. This makes the monk both respect life and dependent on laypeople for their food. This also makes the layperson think about their actions.

I couldn't help but think that such rules actually harm the Sangha by preventing them from operating in present-day capitalistic societies

Present-day environmentally destructive capitalistic societies both tamper with nature's seed stock & diversity and even hold commercial control over seeds & also GMO seeds. The Vinaya rules offer an example of the importance of protecting seeds & seed stocks.

Other parts of the vinaya were surprisingly in-tune with modern sensibilities of social justice and "Twitter feminism", such as the rule forbidding monks from teaching nuns without being first asked.

Women are guests or visitors to the monastic community because, instead of starting their own monastic order, they asked to join the men. Refer to AN 8.51. The men did the hard yards of establishing Buddhism and gain gifts of property for monasteries then the women asked to join. While only senior monks can administer the nuns, it appears the nuns are expected to receive teachings of monks each fortnight. The scriptures say: "Each fortnight the nuns should expect two things from the community of monks: the date of the sabbath and visiting for advice."

It is also ironic radical feminist Western nuns claiming equality & independence also complain when they can't receive teachings from monks. In short, the Buddhist teachings were created by men. All Buddhist teachings are male teachings because the Buddha was a man. The scriptures (MN 115) clearly say an original Buddha cannot be a woman.

It is a right view in Buddhism to acknowledge there is mother & father in life. Any woman that cannot acknowledge & have gratitude towards good selfless deeds performed by men cannot be a Buddhist because they will have wrong view.

Is it permissible for a Buddhist lay follower, one who has taken refuge and has chosen to follow the Eightfold Path without picking and choosing, to discuss certain aspects of the vinaya in a skeptical light, as I have just done?

The Noble Eightfold Path includes "celibacy" in its 5th factor, called "abrahmacariyā". To quote:

And what is right action?

Katamo ca, bhikkhave, sammākammanto?

Avoiding killing living creatures, stealing, and sexual activity.

Yā kho, bhikkhave, pāṇātipātā veramaṇī, adinnādānā veramaṇī, abrahmacariyā veramaṇī—

This is called right action.

ayaṃ vuccati, bhikkhave, sammākammanto.

Therefore, only relatively few laypeople follow the Noble Eightfold Path. As for the Vinaya, it is not for laypeople. However, Buddhist laypeople should at least follow the Five Precepts but are not expected to follow the Noble Eigthfold Path.

The Vinaya is for monks & nuns. It is only necessary for a layperson to know Vinaya if they must regularly interact with a monk or a nun. This said, if this where the case, the monk or nun would instruct the layperson about the relevant Vinaya rules a monk or nun must uphold.

For example, if a layperson irregularly offers a monk or nun fruit with seeds, while I personally don't know the exact rules, I imagine the monk or nun will either refuse the offering or, otherwise, accept the fruit but not eat it (depending on the circumstances).

Or to describe certain texts as mythological or historical disciples as impure?

The Vinaya is designed for purity. This topic has not yet identified anything "impure" about the Vinaya.

I have not taken refuge in the Three Jewels and will not unless I can do so in total sincerity and a pure conscience.

Buddhism is not suitable for everyone. The Buddha said he only intended to teach those with little dust in the eyes. The Buddha often called his teaching 'Dhamma-Vinaya'. The Three Jewels include Vinaya, which promotes harmlessness & renunciation for monks & nuns and, most importantly, ensures appropriate protective boundaries between monastics & laypeople.

For example, contrary to Christianity, the Vinaya ensures there can be no protection of pedophiles and other sexual abusers within the Sangha. Unlike Christianity, which often believes in must exercise Christ's Forgiveness towards a sexually active priest, the Vinaya offers no such option. A monk or nun engaging in any external sexual act is immediately defeated &, when discovered, expelled from the Sangha.

potentially unsanitary?

The life of a monk is to dwell without fear. Monks don't check their alms food for poison, for example.

preventing them from operating in present-day capitalistic societies

Is that not the point of at least some of parts of the Vinaya?

Raga (Sanskrit, also rāga; Pali lobha; Tibetan: 'dod chags) is a Buddhist concept of character affliction or poison referring to any form of "greed, sensuality, lust, desire" or "attachment to a sensory object".... The Abhidharma-samuccaya states:

What is craving (raga)? It is attachment to the three realms of existence. Its function consists of engendering suffering.[7]

Raga is said to arise from the identification of the self as being separate from everything else.

Alas, I only have that book in sanskrit.

CASE 16. UMMON'S SEVEN-FOLD ROBE

Ummon said, "The world is vast and wide; why do you put on your seven-piece robe at the sound of the bell?"

Mumon's Comment: When one meditates and studies Zen, one extinguishes the attachment to sound and color. Even though some have attained enlightenment by hearing a sound, or an awakening by seeing a color, these are ordinary matters. Those who intend to master Zen freely master sounds or colors, see clearly the nature of things and every activity of mind. Even though this is so, now tell me: Does the sound come to the ear, or does the ear go to the sound? But when both sound and silence are forgotten, what would you call this state? If you listen with your ear, it is hard to hear truly, but if you listen with your eye, then you begin to hear properly.

If you are awakened, all things are one and the same,
If you are not awakened, all things are varied and distinguished.
If you are not awakened, all things are one and the same,
If you are awakened, all things are varied and distinguished.

You're being way too literal. The continued execution of religious prescriptions rarely has anything to do with the more or situation that first gave rise to it. Tradition carries it forward, but not without it first establishing something far more interesting in the process. Each training rule is an opportunity to subjugate the ego. Whether it's a matter of how many bowls you own, how you wear your robe, or how you address members of the opposite sex, each instance bends the will away from one's personal concerns and toward the dharma. In following these laws, we forgot ourselves. That forgetting is what's important; most of the rules themselves are almost arbitrary (although let me be clear - some exist that are utterly mandatory).

There's a really great movie entitled Spring Summer Fall Winter and Spring. If you get a chance to watch it, pay close attention to the doors. Every doorway at the monastery depicted in the film can be walked around. They are just doors built in empty space. They don't take one through a gate or into a sealed off room. In practice, there is absolutely no need to use any of them. But all of the monks do (and poignantly, those who have gone astray do not). Training rules are no different than the doors depicted in that film. In fact, the rules are doors themselves. Each one is an almost arbitrary limit that we place on ourselves. Nevertheless, when we choose to take up these kinds of restrictions, they convey us into rooms we would not otherwise have been able to reach.

Only when we carefully put on our seven piece robe can we pass through the door that leads to the throne room of the Buddhas. What does it mean to put on that robe?