[quote=@Zobozun]
That's bull, but sure, accepting your premise of "the soul's autoimmune response" on a purely artificial human, that still leaves Rin transferring her crest to Shirou as well as Surgical Procedure which both show it's definitely possible to ignore that entirely. 
That, and IIRC it was stated one can transfer magic circuits if both subjects in question are synchronized and willing, and a corpse can't exactly resist on either of those fronts.
[/quote]

A soul's a soul. Homunculi still have one.

Rin explicitly processes it so it'll work, since Shirou goes as far to talk about rejection in his mental narrative not much earlier. There are ways to process small amounts of a Crest so that can be received, but even that's just because Crests aren't entirely normal Circuits anymore. There aren't means of doing that for either the entire Crest or someone else's Circuits proper.

You see that with Touko and her butterfly wings, in spite of Touko being so good at familiar creation that she tricked a planet. 

You see that at the end of Apo, in spite of Chiron being a medical genius who transplanted a Servant's heart into a mud doll.

Besides that, if your logic was right then anyone with Spiritual Surgery would be able to just take all the circuits of any dead magus they find without issue. It's not. Transfer of a minute portion of a Crest, which has already been isolated from the whole and isn't Circuits proper anymore, is fine. Transfer of the full Crest or of someone's soul organs, however, is not.