A submarine's a - ah well, I was going to say "boat" but honestly it might be more akin to a very large bus, given you know what that is. It's designed to dive under the water and transport between those docks and the city itself while everyone inside keeps dry.

... As to the cat bus - that thing works in mysterious ways. I had someone confirm to me it helped them get from Willow to Never Fade, so clearly it can either fly or teleport.