Oh, that fic. Eh, I'd rather see a Negi/Chachamaru pairing simply out of the sheer novelty of the idea. After all, Chachamaru is a mechanical being with human emotions, which is... unusual as a love interest. Multi's body is fundamentally organic in To Heart, and the same goes for Nuku Nuku. Chachamaru, on the other hand, is visibly artificial, so one can't just convince oneself she's human - her inhuman nature is made apparent by her looks.
About the only case like Chachamaru I can think of would be Ifurita, whose inhuman nature is made apparent by her absurd power, but... looks-wise, Ifuria appears just odd, not outright nonhuman. *shrug* Am I even making sense?