If I have a Metamorph Alchemist, and they use their shape-shifting powers to assume a form with 2 claw attacks, will taking a Feral Mutagen give them a second set of claws (bringing them up to 5 natural attacks) or will it simply reinforce the preexisting claws?
Yes this is a "metaphysical limbs" question,
no, pick between existing claws or mutagen claws.
So I can't have foot claws?
You can, but you need them to stand. And without the rake ability, there are no common circumstances in which you can attack with them.