Gigabyte saying the cooler is compatible is just one part of the equation...it's also a matter of the socket placement on the mobo in relation to everything else in this small case.
Yes that is correct, they do not show compatibility with cases, just with motherboards. Though they do a remarkable job of testing compatibility with issues like memory and video cards.
I really didn't give much thought to the case, I assumed that if it fit the motherboard, that it would fit the case. I just did a quick lookup of the case, and it sure seems like it should fit.
I do agree with you though that the big noctua is a bit of an overkill. The U12p is a safer choice. An even safer one is the NH-U9B SE2. The best thing about all of them is that when Haswell and subsequent chips show up, Noctua will provide the new CPU mounting kits for free, as long as you save your receipts.