I can't answer you about the windows, but I have some experience with product models at different box stores, because I sold the same products in my store. Take a Weber grill, for example. I sold the standard Weber Genesis. HD sold a slightly different model, Lowes's a bit different than that, Sears had a pin stripe no one else did, and Ace/True Value had some different colors. None of the model changes were earth-shaking. The grill I sold had porcelain coated steel grates; the HD model had uncoated cast iron grates. Mine had wood shelves with a fruitwood stain; theirs was a little cheaper wood with paint. Otherwise, the guts were identical.
Why do they do that? Because of their low price guarantee. They advertise, "Find the same model at a lower price, and we'll refund the difference plus 10%." Of course, you can't find the same model anywhere else -- the one they sell is slightly different.
Now, as I said, I don't know if that's the case with the windows. It's no longer the case with the Webers -- Weber finally tired of the game and started shipping the same grill everywhere. There was no real difference in quality, except possibly for the painted wood shelves.