I was told by apple it does invalidate apple care.
I went ahead and swapped my 512GB for a 1TB. If my machine breaks I'll put a 512 back in before sending to repair. New screws are available cheaply so they won't even look like they have been touched.
I'm actually in favor of Apple doing that. Too many people try to replace parts without knowing what they're doing and accidentally break them. By preventing people like these from gaining access to it, the chances of a user breaking something are down.