I played TSLRCM with Achilles balance mod, so I guess utc files changing Sion and Nihilus
are OK. The basic problem is the handmaiden sister file a_sisend.ncs, which I deleted from the Override directory (otherwise you can get a crash or something). Some of the fights got irritatingly difficult at the end, so I decided to try some different enhancement mods, but maybe the problem was just my choice of equipment or prestige class. In any case, I assume most utc character files are not a problem, although I do not know the effect of the n_darthsion002.utc file on the Atton-Sion fight you get when light-sided (maybe none--I found Sion easy enough for Atton but really difficult for the Exile). I have not actually played through with these other mods yet, so I don't know how they compare.
Edit: I forgot to add that I used VP's Trayus mod which
(I guess) increases difficulty on Malachor, as well as Achilles autobalance.2da