Fairly sure homunculi have weaker individual souls than humans, though, given that's the justification for the crappy od they get. the "autoimmune response" should be weaker as a result.
And as for the other thing does that mean if Rasputin was to process it using alchemy first he would be able to transplant efficiently?

EDIT: Also you're leaving out the part where there's a readily available procedure to make the guy's liver work for you.