In the case where the systems are shipped, it makes sense (cross shipping, so the original system isn't checked, and they don't return such items). Just keep the OEM gear on hand until Apple Care is done, and remove anything you added from 3rd party sources before sending/taking it in to Apple. Don't leave it to chance.They shouldn't be able to do that!
If I get my Mac Pro replaced, they should transfer the upgrades or pack the other stuff up safely in a box and give it to me. There would be hell to pay if they took my SSD (+ Data), graphics card and additional RAM.
I find that really weird, good to know though.
Apple didn't place those components in the system (made any money on them), and won't put any resources into tracking such items down (costs them money). Keeps the margins up...
