For anyone that saw my recent but now gone mod, use PapaZinos Ebon Hawk Repairs instead as they fix the same thing, are much better and the walkmesh was broken with the one I uploaded.
I can't remember my early playthroughs of KotOR 2, but in my recent playthroughs I don't recall ever seeing this issue which is why I was confused as to why it was a thing. Having that mod installed might explain why.
