The Quake 3 Arena Skin Archive has posted a reply they received from id Software's Kenn Scott, who, while temporarily declining an interview offer, does provide an interesting tidbit about Q3A skin editing that I hadn't seen mentioned before:

"...We have seperated alot of characters faces from the rest of the bitmap to make it easier for folks to cut and paste their own faces on clan skins, etc. though it'll still take a lot of art editting to fit. We've done it here a few times for fun (and abuse), so it's not too difficult. :)"