KOS-MOS is a woman shapped robot. I'd hardly call that female in a meaningful sense.
This is both true and misleading. While KOS-MOS is a gynoid, and therefore not female in the strictest sense, she is also the vessel for the spirit of the single most important woman in human history (as far as the Xenosaga Universe is concerned).
This is a moot point, however, since Samus could take her anyway.
(Hmmm, now that Nintendo owns like 80% of Monolith Soft, maybe we will get to see KOS-MOS vs. Samus in a future Super Smash Bros game. Its more likely than a Chrono character in any event.)