Why Comfydants are okay with cannibalism

Comfydants come from a time when animals were all but extinct. Cybernetics were needed on a basic survival level, so amputations and such were common. On the more extreme end, it's even possible that the brain alone is the only organic part of a person's body. Simply discarding the removed flesh/bones/etc from these surgeries would've been seen as a massive waste of an extremely rare resource, so the parts are made use of. Flesh is eaten, bones are used to make bonemeal, skin might be processed into leather, and so on. It's a practice that doesn't affect anyone other than Comfydants themselves and individual people who may come to the Comfydants to get cybernetics of their own. I imagine the practice would be seen as disgusting to most outsiders, but they also have very little reason to actually care about a purely internal practice enough to ostracize a useful ally over it.

Why are enemies and prisoners not eaten? If human bodies are considered a rare resource in their timeline wouldn't their culture encourage not wasting any of it?

Free will is tantamount so they wouldn't be taking prisoners in the first place, they'd be killing enemies in the field directly, unless extenuating circumstances made taking a hostage absolutely necessary. This brings us to the problem: they don't know where the fuck those enemies have been. Who knows if the meat is safe for consumption? It could be radioactive, carrying toxic levels of pollutants or riddled with disease. All very big problems in a world where pollution is so bad life can barely exist in it. Better not to fuck with mystery meat. If they have enough time, they'd harvest the skin and bones for later potential use, but for the most part Comfydants serve best as scouts and saboteurs. These are not positions that lend themselves to leisurely staying around to dress carcasses after a kill.