Since it is likely that many dogs who you don't know the vaccination status of have been in that room, I would not let him out in the pet room. Leave him in his crate. 1.5 hours isn't that terribly long, so as long as you make sure to give him a potty break before you board the ferry and perhaps play with him a bit before to tire him out, it's likely he'll just sleep the whole trip.
A short trip like that isn't likely to cause any severe setbacks. Worry about getting him home safely first, then worry about starting on training.
A short trip like that isn't likely to cause any severe setbacks. Worry about getting him home safely first, then worry about starting on training.