You can make places walkable by setting them above or below ground level by a small amount (> 0.1 iirc), and then using invisible wall places to block where you want to block (don't go too crazy with them of the pathing lag will be bad).
As for the tiles, I can think of a number of solutions. Flat tiles, like a city cobble tile, don't have much z, and are suitable for putting water tiles over. Or, you could use tile editing to put in totally invisible tiles, though that's more technical.
Or, there's the simple approach. The very first PW I played on had something like this, and they just had all the spawns spawn onto the boat, having 'jumped on board' from the water already, using a bioware ship tile group.
Funky