ok, so ive been doing more testing, and ive discovered that this phenomena is not actually unique to this sub-mod. this actually does affect the vanilla mod, its just not as noticable. started up a game playing as the lengi empress to check if the standard westerosi sprites was used on the other side of the map, which is supposed to use eastern sprites(the turkish ones i think.)but instead, both vassal levies and retinue also use the standard western style sprites.
after a reinstall, i decided to test a bit, and i discovered that if you only edit the base files to have all provinces have 7 holdings, but leave the unbuilt cities/castles/temples(all the new possible buildings were added by another sub-mod) alone so they arent there at the games start, then you avoid the override sprite problem.
so if you want to have more buildings possible than the regular mod, it seems you can do so and avoid the sprite override, by making sure no extra buildings are added at the start. im not sure if this problem will persist as the game goes on(and the extra holdings are filled out) but ill edit this post and add my findings.