Just out of curiosity, why are most of the rebel skins and many others basically transparent?

The Modding FAQ is very much your friend.

http://www.gametoast.com/forums/viewtop ... 27&t=21268
http://www.filefront.com/9755495/tut3.wmv

Written or video tutorial, take your pick.

He asked *why* not *how* Unless I'm mistaken the tutorials don't answer that. I'm curious myself, as far as I can tell there's nothing transparent about them, so why is there transparency on them?

The transparency is an alpha layer. The alpha layer controls the intensity of the specular map. The darker the alpha layer the less shiney the model will be.

If for whatever reason you decide to remove the alpha layer then you'll also want to hex out the specular enabling part of the material within the msh, for example in Material71 for all_inf_pilot.msh: ^Change:
04 00 00 00 80
to:
04 00 00 00 00

or for another example cis_inf_bdroid.msh, in Material1 you'll want to change:
04 00 00 00 00 04
to:
04 00 00 00 00 00

Leaving the specular flags in the msh without an alpha channel in the texture may result in an extremely shiny character ingame.

http://www.gametoast.com/forums/viewtop ... 20#p279620