That might work.
Second dumb question, how do I reference the *.nif and *.dds files without having to unpack everything? (or can I)
No need to create a script extender dependency for that.
if you mean adress direcly a vanilla mesh in the .bsa just create a directory in your data folder with the exact name of the one you want to use (eg clothes\lowerclass) and place a dumb file with the name of the cloth you want to use. Then in the cs choose this file. When done, delete the directory and he game will return to the default path (in the .bsa).
I did the reverse, changing all clothesin game to armor (so the NPC can remove them at night and wear only their basic undies to sleep ) using exactly this method. Same for the icon and the .gnd. You just have to copy/paste the model from the armor to the cloth model. Very simple and fast