xD Basically, autofeed is a botting program that automatically feeds your pet when it hits a certain hunger number. It's not that hard to get away with, as Aric says, considering it's not something many people notice, and it really doesn't effect anyone else. Technically, it's still illegal, since it's still a bot, but... Meh. xD The chances you get caught is slim. Still, I never used one just as a precaution.
Yes, I'm sure it'll work for feeding the homunculus too. Hell, if you look around long enough, you might find someone who scripted an AI system that makes you autofeed them. o.o Since there are AI's that make your alchemist automatically pot your homunculus when it gets to a certain percentage of HP, I don't see finding an AI for autofeeding along with everything else all that hard to imagine.