The Origin of Flesh
The protagonist's ability to purify means that nothing of his victims but the Idea Sefirah remains, beyond a few blood spatters created during the fight. That means that when Grotesques drop items, those items must have been things that they were carrying on them (and therefore would not be part of the data that comprises their crystal). So since the flesh you consume isn't being butchered by the player, it has to be being butchered by the Grotesques themselves, right? The problem there is that Grotesques don't fight each other outside of occasional and accidental friendly fire. This means that the flesh you're eating isn't from the Grotesques. It's likely from the numerous clones of Number 12 that previously died in their mission. Number 12 is probably eating himself.
More evidence for this theory stems from the bizarre names of the flesh cuts: Idiot Flesh, Average Flesh, and Genius Flesh. The further down the Tower you go, the more likely you are to find progressively "smarter" hunks of flesh. This would make sense if this is Number 12's flesh, since the depth each clone reached would serve as an indicator as to how "smart" that respective clone was. You do occasionally find smarter flesh early on and dumber flesh further down, but luck can play a big part in Baroque. This theory is also thematically faithful to the survivor's guilt the protagonist feels. He believes that he is unworthy of life, as his twin brother was sacrificed in order for him to live. Surviving the Nerve Tower only by consuming the flesh of his mirror copies is fittingly ironic in this light.
Have you noticed that while the weapons and tools you use harness the elements of ice and electricity, the bones you find only ever produce flames (besides those steeped in the ailments that likely killed their original owners)? The Archangel’s constant insistence that the Great Heat Wave is Number 12’s fault would likely have a strong distorting effect on Number 12’s mindset - and therefore physiology. As he believes himself to be the source of the cataclysmic heat wave, the Burst, Homing, Silver and Gold bones that unleash waves of fire suddenly make a lot of sense. Some doubt is cast on this theory by “Baroque Report Gold” however, as while its author states that the bones coming from dead clones is a possibility, they also state that the bones could come from "Grotesques who failed to fully purify". This is an equally valid conclusion, as when Grotesques drop items, they don't drop Idea Sefirot (possibly signifying that they weren't fully purified). Like many things in “Baroque”, the significance of these elements is left up to the imagination of the player.