Why certain character was kidnapped

So, one thing that bugs me is why Geppetto was captured by the Alchemists? I don't mean it from storytelling perspective, because it was obviously done to raise the stakes, but from the story logic. 

I don't think Simon wanted to lure P onto the island - he didn't need him for anything and besides, P already intended to go there.

Another possibility is Arm of God artifact, but, if I'm not mistaken, Simon already had it. AoG was stolen from the island by the archbishop, then Geppetto got it and then it was taken by Simon from the train cart where P awoken. At least that's how I understand the letter he left. Or am I wrong and Simon learned in the cart that Geppetto has the arm and that's why he organised the kidnapping?

What do you think?