So I recently chipped an apex seal, which took out the rotor and housing. I'm seeing some FD housings for similar price and and quality as FC housings. Can you interchange them?

I know that the spark plug locations are slightly different from S4 to S5, but it looks like S5 and FD are the same. Apart from that, the FC housings have the water jacket opening to feed the turbo through the LIM. Thats only necessary for the rear, though, so my existing housing will still do that.

Apart from those things, are there any reasons I can't use it?

Next questions, since we're here, is there a difference between S5 turbo and FD rotors? Appear to be same compression ratio and weight. I've heard FDs actually have a thinner casting at the facings which can dent in very high boost. Just trying to keep my options open.

 

S5 TII and FD rotors and housings are functionally identical and completely interchangeable noting the water port you highlighted. Only difference you didn't mention is the apex seal surface anti-friction coating is a 'better' graphite type on the FD (which is why they cost an additional arm & leg from a new FC variant).