Okay, here's my two cents worth -
I'd put the burden on Apple. It shouldn't matter where you buy your Applecare - from a retailer, from eBay, or from the next door neighbor's kid who picked up a bunch of Applecare packages cheap when the local home electronics store went out of business. If Apple wants to ensure that you purchase only from an authorized retailer, then then they have the option of insisting - at the outset - that you send in a copy of your receipt in order to register your Applecare.
If Apple does not demand a copy of your receipt at the outset, the question then arises whether they can demand it later - after they've already accepted your registration. I'd say no. Here's why: you relied on the confirmation email you received from Apple in concluding your eBay transaction. Based on that email, you (presumably) left good feedback for the seller (which you can't later rescind), and you declined to open a case with PayPal. Your reliance on Apple's confirmation email should be enough to protect you.
In other words, you were damaged not because you were scammed by the seller (if, in fact, that's the case and there wasn't simply an honest mistake) - but because you relied on Apple's confirmation email which told you that you had purchased and registered a valid Applecare registration number.
If Apple has a problem two months down the line when someone else tries to register the same number, that's Apple's problem. They can, at that point, demand further documentation from the new registrant. If the new registrant is able to provide it, then too bad for Apple - they'll need to honor both. They can't come back to you two months after the fact and say "oops" and expect you to suffer because of their mistake. And if they accepted your erroneous or fraudulent registration, it is their mistake, not yours!
Sure, if they can prove that you deliberately defrauded them, then they can come after you. Otherwise, they're on their own. They either set up stricter standards for registering Applecare in the first place, or they accept the consequences when something like this happens.
Go back to Apple, and when they blow you off, just keep going up the chain until you find someone who will listen. And, keep this in mind, you're doing them a favor - Apple can use any information it can get about unscrupulous sellers of Apple products. You provide Apple with information about your transaction, you are helping Apple to prevent future fraud. They do have a fraud prevention unit and they do care . . . so see if you can't make this a win-win situation for you and Apple!