The much stronger position is that prejudice based on immutable characteristics is bad, period, but that prejudices harm different groups to different degrees.

This isn't much stronger.

If "misandric" beliefs save a woman from being beaten, r*ped, or murdered, the belief has served a beneficial social purpose, even if the emergent behavior is socially harmful.

(I understand every racist is itching to repackage this argument)

Prejudice is just a stand-in for knowledge. The lack of (or aversion to) knowledge is the actual social ill.

Racist tendencies, both individual and systemic, can arise without prejudice. Racism isn't just emergent prejudice and would still exist if all prejudices were wiped from people's minds.