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.