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As mentioned I haven't tested them to compare them. So you'd have to check it yourself. However, while the Detoxifier Kidney has a lower efficiency the bonus stats will probably put it higher because straight stats typically offer larger bonuses than what the efficiency percentage offers.
I have to tell you I love the organ transplant part of this game. I have Cystic Fibrosis and had a double lung transplant, so it makes me feel at home :)
The bionic kidney simply improves kidney function which improves Blood Filtration and Immunity Gain Speed. The Detoxifier Kidney also provides Toxic Resistance, I never checked how it compares in terms of Blood filtration and Immunity Gain Speed but its probably a bit better.
It's been asked a number of times but I don't have any plans to add them.
That's vanilla behaviour and this mod does not make any changes to it. A Prosthetic Arm which is also vanilla replaces the shoulder, arm, hand and fingers. If the shoulder is still attached the game might be stupidly considering you replacing the limb rather than giving them a full new limb. There could also be something with Ideology or Traits where they don't like non natural things. It could also maybe be due to the Prosthetic Arm having a worse efficiency than a normal arm.
I haven't dabbled much with patching up NPC pawns with prosthetics so I'm not sure about the specifics of what is allowed and what isn't. There should be a mod or two floating around to remove the restriction if need be although I don't know the name of any offhand.
If a prisoner has a missing arm, and I surgically attach a prosthetic arm, I am getting unhappy faction: harmful surgery performed on member.