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I think I agree Geoff. The "brain rule" that exercise is good does seem independent of the assumption that the brain is not evolving. The text of the Brain Rules book does seem to make that assumption, though. If I recall correctly, though, some of the other "brain rules" may rely on the assumption that brains aren't evolving.
Either way, my linked-to post was meant as a general discussion of the conflicting views of whether or not the brain is evolving, and not meant to specifically address exercise in any particular way.