Yeah, there is no way you can fit a Gen 2 battery into a Gen 1 battery as-is--but there is also the issue of reprogramming the Gen 1 to work with the Gen 2 battery. I remember someone a while back exploring this and hitting serious roadblocks due to software incompatibility. What we need is for the OP to post the repair order and some actual numbers to get to the bottom of this. I would like to see what kind of reprogramming was done and what other parts were replaced--some Gen 1 parts would absolutely have to be modified for this to work.
While I really, really, want to believe this is true, I'm not grabbing the popcorn and hoping for a battery failure just yet. I mean, it's only been a couple years since Gen 1 was discontinued. Would GM have already "run out" of Gen 1 refurbished batteries? The replacement does not have to be "new" according to the warranty. While not likely that GM would keep a large inventory of Gen 1 batteries in cold storage for a decade, I would imagine that there is still a healthy inventory of Gen 1 batteries still available now. But heck, who knows.