In Europe, do trains/buses get transported by ferries with the passengers inside?

Everyone has forgotten the Sicilian train-ferry?

Trains from mainland Italy to Sicily are taken on a ferry between Villa San Giovanni (mainland) and Messina Maritima (Sicily).

Video: here and here and many others on Youtube

Seat61 page: https://www.seat61.com/trains-and-routes/trains-to-sicily.htm

Currently, the trains that use this route are:

• ICN 1955 Roma-Siracusa, Villa S. Giovanni d 03.50 – Messina Centrale a 05.15
• ICN 1959 Roma-Siracusa, Villa S. Giovanni d 06.35 – Messina Centrale a 08.05
• ICN 1963 Milano-Siracusa, Villa S. Giovanni d 11.05 – Messina Centrale a 12.45
• IC 723 Roma-Palermo, Villa S. Giovanni d 14.30 – Messina Centrale a 15.35
• IC 727 Roma-Siracusa, Villa S. Giovanni d 18.25 – Messina Centrale a 19.35

And in the opposite direction:

• IC 728 Palermo-Roma, Messina Centrale d 10.10 – Villa S. Giovanni a 11.20
• IC 724 Siracusa-Roma, Messina Centrale d 13.10 – Villa S. Giovanni a 14.20
• ICN 1962 Siracusa-Milano, Messina Centrale d 16.45 – Villa S. Giovanni a 18.15
• ICN 1956 Siracusa-Roma, Messina Centrale d 22.10 – Villa S. Giovanni a 23.35
• ICN 1960 Siracusa-Roma, Messina Centrale d 00.35 – (passing through Villa S. Giovanni) – Salerno a 06.42

(All times from Trenitalia pdf timetables "In Treno Tutt’Italia")

The main ferry link between the UK and Republic of Ireland for passengers is from Holyhead to Dublin. Other routes include Liverpool-Dublin and Fishguard/Pembroke to Rosslare. This answer concentrates mainly on the Holyhead-Dublin link, primarily from to personal experience.

Trains

While there are rail connections to all the mentioned UK ports, no railway carriages are carried on board ferries. The main reason for this is that Irish railways use a different track gauge.[1] If you took a carriage onto the ferry, you couldn’t take it any further than the other port. As a result, passengers travelling by railway are expected to alight the train and then embark the ferry themselves.

At Holyhead, the platforms of the railway station were placed along either side of the inner harbour[2], this allowed a cross-platform interchange between boat trains and the ferries. This arrangement survived until the late 20th century, when larger ferries (suited to roll-on-roll-off vehicle traffic) were unable to access the inner harbour, and new gantries were built in the outer harbour instead. The railway station and platforms remained in the same place, however. The gantry built for Stena Line’s HSS Ferries in the 1990s was relatively near ferry terminal, and foot passengers could walk the short distance. Current ferries have gantries further out, and foot passengers are shuttled to the road deck of these ferries by a bus, and passengers then climb the stairs to the passenger deck. The bus does not sail with the ferry: it is removed before the ferry sails.

On the Irish side, there is no rail connection to Dublin Port. (The nearby port of Dun Laoghaire has a railway station, but ferries stopped serving this port in 2015.) Irish Ferries have gantries that include a gangplank for passengers to embark and disembark directly from the passenger deck, though some moorings require passengers to embark/disembark via the road deck. Stena use a shuttle bus between the ferry and the passenger terminal, as at Holyhead.

I understand that Rosslare’s railway station is close to the harbour, as is Fishguard Harbour station. Pembroke Dock station is a short walk from the harbour. As above, passengers will walk from the railway station to the ferry terminal.

Buses and Coaches

There are no timetabled public bus services between the Republic of Ireland and Great Britain. There is a limited scheduled coach service[3], and some private coaches will operate. These drive onto the ferry with other road traffic, but will be subject to the same regulations as other vehicles, which require all passengers to leave the road deck and remain on the passenger deck while sailing. Passengers will presumably return to the coaches at the same time that car passengers do, on approaching their destination.

Foot Passenger Numbers in General

The growth in use of roll-on-roll-off car ferries, and cheap short-distance air travel, means that foot passenger traffic (e.g. from rail connections) is greatly reduced compared with decades ago. As this is a shrinking proportion of ferries’ business, it does not warrant any significant spending on new infrastructure for foot passenger connections.

[1]: This was made law by the Railway Regulation Act of 1846

[2]: See https://www.flickr.com/photos/blue-diesels/5862917181/ for an example of how close the railway and ferries were

[3]: National Express offer coach travel between London and Dublin: https://www.nationalexpress.com/en/destinations/dublin/london-to-dublin

As with the general big areas questions the answer is ‘it varies’.
With the longer crossings, where buses go on car decks below the waterline there is a common rule that all passengers, including drivers, have to leave the vehicles and go to the same decks as foot passenger. A general rule but I have heard about exceptions on this as well.

On most crossings train passengers will use the ferry as a foot passenger and the train will not enter the ferry. Some long distance bus lines work with this system as well.

On some smaller crossings local buses may travel on the deck of a ferry in which case the bus passengers stay in the bus.

There are or were a few ferries which did transport trains on the ferries, I remember one between Germany and Copenhagen, it may have been within Denmark, where the train drove onto the ferry and the train passengers were given the option to stay in the train on go out onto the ferry, most of the ferries in Denmark are replaced by bridges and this line is one of them.
It used to be more common in the past but it has not been the case for most lines that used to do this for a long time. And I doubt it has ever been between Ireland and Great Britain.

So if you travel by train and ferry prepare for walking off the train onto the ferry, if you travel by coach / long distance bus, expect to leave the bus on the ferry but you might also be asked to walk onto the ferry with your luggage.