> 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.