How should a Protagonist defeat an Antagonist? Is it after they have resolved their flaw (conscious or subconsciously)? Is it before or after they have changed, or is it by using their new knowledge/experiences?

"Flaw" is the wrong term. Limitation is better. There is more than one flaw / limitation.

Lots of flaws / limitations are overcome. That's one function of the journey through the New World.

The condition for final engagement is that the hero has changed and gained new knowledge and experience. That's another function of the journey through the New World.

The function of the final battle is to force overcoming of the most potent / fearsome flaw / limitation.

In The Shawshank Redemption (1994), Red’s greatest fear is not the prison, not the warden and not Hadley, it’s freedom after years of institutionalization.

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