Is there a higher alaya in Vajrayana?

Is there a higher alaya in mahamudra that is separate from the lower alaya the vijnana skandha?

Vajrayana is a term used to denote Tantric Buddhist schools.

Practitioners of those schools might have somehow different views.

For example, Gelugpa School is based on teachings of Atisha, who was a legendary teacher of 11th century, famous due to his outstanding practitioner's skills, modest and kind personality, and deep understanding of unity of Buddhist Sutric and Tantric teachings.

Atisha wrote a "Lamrim" ("Steps of the Path"), explaining all the Buddhist theory and practice, including Tantric practice, as a unified system.

Later Tsongkhapa based his larger treatise on Atisha's works.

According to their views, Tantric Buddhism means using specific (Tantric) methods for realization of usual (Sutric) concepts.

So in terms of teachings, there is no essential difference between Tantrayana and "Sutric" Mahayana.

Mahamudra is just practical realization of the wisdom of emptiness, expounded by Mahayana teachers such as Buddha Shakyamuni, Vimalakirti, Nagarjuna etc. In Mahayana, those teachings are classified as "Maha Prajnaparamita" class teachings, i.e. teachings about The Great Perfection of Wisdom. They include "Vimalakirti sutra", "Diamond sutra", "Heart sutra" etc.

Madhyamaka school, stemming from Nagarjuna works, is the most focused on prajna paramita teachings.

The model of Eight consciousnesses, where Alaya vijnana is the eighth, is considered belonging to the Vijnanavada school. See "Lankavatara sutra".

Though there were Buddhist teachers criticizing Vijnanavada views, e.g. Chandrakirti, their criticism actually does not refute Vijnanavada views; only primitive ways to understand Vijnanavada views.

So both Vijnanavada and Madhyamaka views are useful and are studied in some Vajrayana schools.

I don't know any specific interpretations of Alaya vijnana by any Vajrayana teachers which would differ from views of those Mahayana schools.

There are some practitioners who would deny the unity of Sutra and Tantra, and could even claim that "Sutric Buddhism" is inferior, but upon investigation such views never hold water.

Such views actually come from lack of prajna, from absolutization of notions, for example, categorizing Buddhism into different parts and levels. Such categorizations are just concepts, relatively true in particular regards and particular limits, nothing more.

So those people may claim that they represent, for example, Nyingma school views, or even something that goes beyond the limits of Buddhism (Dzogchen), but in fact "Sutric" Buddhism is well aware of limits of words and concepts, and goes beyond them itself.

As far as I know, Padmasambhava, from whose teachings and activities Nyingma school has developed, did not contradict or modify usual Mahayana teachings.

With all that in mind, my answer is:

I don't know of any ideas of "higher alaya separate from the lower alaya".

That would be a strange idea, because the concept of alaya represents the highest level of inseparability and non-conceptualization.

Let's examine your expression, "the lower alaya the vijnana skandha".

Vijnana skandha is a concept that describes the reactive nature of mind.

We can talk about my personal mind, your mind, and minds of other beings. Also, we can notice that all things in the material world exhibit the quality of reactivity. We could generalize and say that all the world has a nature of reactivity, and it goes beyond and in between of sentient beings. In other words, reactivity does not belong only to sentient beings, but it's a nature of everything.

We can see everything as reacting and happening beyond limits of individual minds. Thus the notion of the all-encompassing, universal mind, alaya, can be roughly understood.

But it's just our notion. We take various phenomena, we group them and create notions. That's how our notion of mind appears, for example.

In the direct perception there is no "mind". The mind, or consciousness, is a concept created by dualities like perceived and perceiving.

Trying to liberate our minds from the slavery of absolutized notions, we can try to see our concepts as relative. We can say that in the original perception phenomena just appear; they aren't divided into the perceiving and the perceived.

That original non-divided phenomena can be viewed as the reactive space, and conceptualized as vijnana skandha or Alaya.

But there is no actual "vijnana skandha" or "Alaya" in the original direct perception; those terms are concepts or images we use to understand.

The actual reality isn't grasped by such concepts, or any other concepts; concepts are, in the best case, pointers at the experience.

So we use terms like "vijnana skandha" and "Alaya" in order to get close to the truth, but they never actually encompass it.

It's like using items on your boat in order to point at something in the surrounding ocean; they don't actually exist there in the ocean.

So speaking about some higher alaya or higher vijnana would be like trying to add more things to the things that can't capture the ocean.

Our items on the boat can't capture the ocean, and if we therefore try to add more such things, it's of no benefit.

To get closer to the truth we should instead try to grasp how concepts are relative; how pointers at the reality aren't what they point at.

Then we could understand and use concepts properly, and manifest Mahamudra in practice.