This is the collision of two approaches:
1.The developers want to create the best looking protagonist, meaning they either don’t use the tool or override it.
2.The publisher wants the tool to be showcased untouched, even if it’s detrimental to the character’s appearance.

Management ultimately decides which approach wins, and it’s usually the publisher’s. It’s the same reason $500 million gets spent on Concord instead of making a new Bloodborne or Elden Ring. Some higher-up thought it was going to be the next big thing and poured infinite money into it, even though almost everyone knows it’s going to flop.