DCSS has only ever had about 4 meaningful mutations at a time. If it's not robust/frail, slow/fast movement (rip), or wild/subdued magic, it's either a minor convenience or a minor to moderate annoyance, and the only way it will change the outcome of the game is if you forget you have it - see literally every blurry vision or low device heal related death. And getting mutated involuntarily before any cure mutation is available is very rare; it basically requires early banishment or Xom, especially after monsters with wands of polymorph were changed to not mutate you, and especially since cure mutation's frequency was increased, and especially since new !mutation which is far too good - my characters have good mutation sets for the entire post-Lair game now, thanks to ugly thing spam in late D, Vaults, Depths and plentiful !mutation to refine them.
Ideally temporary mutations would just die and only species/Ds/Ru mutations would be left. My last game had
104 mutation changes and I only briefly worshipped Xom. It's an obnoxious minigame but playing it offers +30 max HP or a huge spellpower bonus so I feel obligated to play it anyway - like how portal vaults are annoying, but they're free items and xp so skipping them is painful.