I don't think it's as bad as all that. I don't recall them ever saying that you could literally buy most of the games on the aftermarket, it was always that as long as you bought most from them and just had to fill some gaps, they would allow it to count.
They definitely said that where you got them didn't matter, but that you just needed to own them all ("own" being the key word and likely what a lot of followers latched on to). They've been hinting at this for about a year now so i can't find the specific tweet/post/etc. where they disclosed that, but they've definitely been a lot more vague on it recently saying things like "details will be announced closer to its release", "we haven't decided how to verify yet", etc. In one of their fireside chats, Josh plainly said he hates talking about it because of all the speculation and questions it has led to already.
Edit: Here's a direct quote from their customer service after the announcement (which was after last year's E3 presentation, in case anyone was wondering):
In regards to the free exclusive, a full set (platform specific) would be 1 of each title whether it is standard, a variant, or a CE whether it was purchased directly through us, or otherwise acquired.
For the Vita game, it'll be a full Vita set.
Later on, it sounds like we will be capping off other platforms similarly.
Have they even officially announced anything yet? I know Josh and Doug have been casually talking about it on Twitter or whatever for a while now, but I think that's been it. Until they make an announcement as a company it's probably a good idea to remember that nothing is set in stone.
They've affirmed that it's happening several times, but they haven't officially said what it is, when it's releasing, or how they'll verify; just that you need to have a full set and won't be able to purchase it. At the LRG party last week, someone found a LRG#000 release for Revenge of the Bird King and posted it on Twitter, which more or less affirmed that's what it will be, but they haven't officially commented on the post.