The Tavern

Being always resistant to mutation and terrible transformation apptitude is penalty since beneficial mutation potion and lichform
So I think it would be better if halfling can control their own mutation resistant level with transformation apptitude.

Having a terrible transmutation aptitude is a small penalty, but not because of lichform. There are a lot of better transmutations at lower levels. That's not an argument to change it, though: some races have penalties. Being resistant to mutation cuts both ways: obviously there's a benefit and a penalty, and in many games neither one is particularly relevant, since beneficial mutation potions are quite rare and mutating monsters only appear near the end of most games.

Halflings are fine

"I don't like that this race can't do this one thing well, so change it."

Is that accurate?

See the readme, in particular there's no attempt to explain why this would be an interesting or worthwhile change.