Oh sure SP mods can be done, but not heavy code modification.
Yeah i said root but you knew what i was talkin' about
I see a few benefits to segmenting models, 1st one is a workaround to the 500 vert limit, dismemberment for player models, destruction of objects, mixing character body parts with others without redoing the weights...so any of those reasons could be valid.
You could try to do it one piece, but if you get really overboard with vertex count, it could get rejected by the compiler, hence the need to segment stuff like wings, horns and other parts until you can reach an acceptable limit.
The hierarchy is usually main groups that always remain the same, head, torso, hips, l_leg, r_leg, l_arm, r_arm, l_hand, r_hand etc. Any other extra meshes receives the name of its parent mesh, so in your case you could have torso, and torso_wings linked to it. head_horns would be linked to the head and so on.
However, when making your own .GLA you should be able to name your asset the way you want, because you are generating the animation yourself and do not have to match a pre-existing .GLA. Personally, i prefered to keep using similar naming convention as the game since i was used to working with it.