At one point, I believe in the context of removing the Fetts' jetpacks, I believe it was mentioned that the stock meshes that came with the game could be hex-edited to accept alpha textures (i.e. transparency). What should I be looking to do to edit a preexisting mesh to make it accept transparent textures?

The Mandalore model in the Conversion Pack KOTOR sides might help. Ask Teancum for it, I'm not sure if it's in the source files thread.