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The ship didn't seem to be terribly specialized beyond the Invisible Umbrella system. That said, as pirates they wouldn't be experienced in large-scale battles. Natora, for all her ups and downs as captain, does have that experience, as does her crew. They could've mentioned it as such, but to me it makes sense that she'd take over so that the Baronche, which as we should remember has her people in it, whom she feels responsible for, has better odds of survival in the final battle.
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