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In echoes of eternity there is a section where Angron eats a guard commander.

It goes into detail about the guardsman still being alive through the process, then goes on to detail how Angron's physiology was recreated by Khorne to be a daemonic version of human anatomy and describes what happens to the body being digested rapidly inside of Angron. In the end flesh and meat is rapidly digested leaving bones (specifically a skull).

Does that skull get digested, or would that anger Khorne?

Does Angron poop out the skulls, or does he have some kind of closed digestive system?

No. Just no.