The LOFTs of the craft map are fine (see attached images). They ought to block shots and line of sight, and in this case some tiles (windshield) can be destroyed revealing some damage below.
What I mean for fake 3D is the ISO image was cut apart to give the illusion that there is a craft on the map. This means some tiles have "objects" that aren't such but just pieces of imagery to when put together they look like the craft. These are often done for the details that are on tiles away from the player (e.g., North-West). And in this particular model, the trick was used to avoid the need of making a detailed second level on the map. To avoid breaking the illusion, these tiles are given 255 of armor so they aren't destroyed easily.
A "true" 3D would imply cutting the model in blocks (1x1x1.412) where the tiles would be and then assemble the images from said blocks. I believe this is what was done on the OSPREY model that is on the forums.
Indeed crafts could be created from 2D pictures, with the restrictions outlined above.
