That would be much worse for passengers who can normally just sleep through the whole thing, it would take much longer to do the transfer, you'd need a larger and more complex ferry with bathrooms, seating, luggage storage, and more staff to deal with the guests, you'd need to deal with scheduling issues (what if you get to the other side and the train isn't there yet?).
I have taken this train and it would have been a nightmare to wake up everyone at like 3am, get them and all their stuff out and onto the ferry, and then do it all in reverse on the other side. It would add at least an hour to the trip if not more.
> you'd need a larger and more complex ferry
Don't those already exist? I don't know, but I assume that regular passenger ferries operate on this route, no?
> it would have been a nightmare to wake up everyone at like 3am
I presume that if one were offloading passengers onto an existing ferry one would not schedule the train to arrive during normal ferry operating hours rather than 3AM.
I think the right answer here is that Sicily is bigger than I thought, about 100 miles across, and so the onward travel time can be significant, and so if you're going to offer a night train whose final destination is (say) Marsala then putting the train on a ferry in the middle of the night makes sense.
When I took the Germany to Denmark crossing I'm almost certain you weren't allowed to stay on the train. I certainly didn't anyway. But, yes, it still saves a lot of time compared to walking between train and ferry twice.