The problem is the floor isn't flat. There are various plates/panels and so forth stacked on top of the base floor. The walkmesh is flat, because adding small rises in it would cause all sorts of problems with pathing and getting stuck. So the end result is that feet clip through anything higher than the walkmesh. It's not super practical to solve without remodelling half the game (it's not a problem restricted to the Hawk).
The new pic looks fine.
Edit: And re: the GIT, that's the primary (along with the IFO and ARE) file that defines the content in a module. It's where you define where all the creatures are in the module (which is how you have a bunch of enemies but only 2 generic enemy UTCs), where all the placeables are, where all the cameras are, where all the doors are, etc. I'm sure there's a module tutorial lurking somewhere in Lucasforums' dead husk that holds the answers you seek.