I'd add that you should save any pdf instructions you found from apple at the time and print to pdf any webpages regarding this swap. Make sure you get the name of anyone you talk to on the phone. The issue is this:
User Replaceable DOES NOT mean User Upgradeable. The instructions state that you are installing a replacement drive. It doesn't talk about the caddy right? If it does then it's fine, but be careful about the definitions you see.
The iMac G5 User Installable parts instruction guide for hard drive replacement stated that removing any screws other than the (IIRC) gold ones would invalidate your warranty, or something to that effect. Meaning that the drive caddy wasn't supposed to be removed from the drive so any replacement would be an Apple vended drive. This seems close to the same situation.
A few calls to Apple representatives cleared that up, but just be aware that replace, upgrade, and install do not mean the same thing.
Apple is correct in what portions of the repair they invalidate. You may want to look at this info about warranties before proceeding (US)
http://www.ftc.gov/bcp/conline/pubs/buspubs/warranty.htm
If your optical drive scratches disks it can't really be blamed on your hard drive. That kind of thing is exactly why the Magnuson Moss Warranty Act was passed.
Good Luck,
-j