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.
Rin made a contract similar to a familiar with Shirou so that it could happen without killing him. Even inside a same family transferring a magic crest can kill or cripple someone if it's not made right and that's because the circuits share your blood, foreign circuits are pure poison.
BTW, the procedure Rin made with Shirou is possible to any decent magus, t's just that if you don't have a Servant worth of Od to spare, you'll screw yourself while giving someone else the power they need. Even Rin got almost screwed when Shirou activated UBW, for God's sake.
EDIT:
Archer's arm also killed him, because the circuit came from a Servant's body. After Kotomine performed the surgery Shirou could already be considered a walking corpse, it was just a matter of time before her became a corpse corpse.
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