If you're under warranty (or Applecare,) cracking the case technically will void it - there are too many things you could damage while you're MBP is wide open which could cause other problems, so even if you do it perfectly... if Apple can tell you've been in there they could just refuse you coverage - so it's a risk.
I just had mine replaced with a WD500, and paid a certified Apple service center (not an Apple store) to do it for me, and asked the tech just these questions. I'm not sure how true this is, but he said there are some little seals that are broken when the case is cracked open which are replaced with new ones... but he told me that if I brought it in (to him, not Apple) for a GPU issue in the future, he'd not even give the hard drive issue a second thought, but go straight at the problem. If I send it directly to Apple, I'd be risking having my replacement drive and any memory upgrades removed and the laptop returned to its 'original' configuration as part of their 'repair.' Also, if I replaced the drive myself in the future, as long as I brought the laptop to him for Applecare service (and hadn't actually done any damage...) he'd be okay with it. If I send to Apple, and they see unauthorized entry - then the user becomes the scapegoat, and the warranty is kaput.
I guess the whole thing can depend on who you're dealing with and how reasonable they will be if you encounter future issues with you MBP. I think it will be a huge advantage to actually know the person who will be servicing the machine - if that's possible. If they realize you know what you're doing, you can probably do a lot more "self-service" without getting into trouble. Just keep in mind as I mentioned, that all of this does come with some risk to your warranty/Applecare plan. If I were you, I'd talk this issue up with a few Apple-certified service centers - speak to the technicians and get some feedback. You might find someone who will work with you much more individually and reasonably than others.