Yes, I watched the video. You are right, the cutout won't work for certain combinations of motherboard and brackets.
I have the HAF-932 and the EVGA Classified motherboard, and in two years, I switched out the motherboard once. For the switchout I had to take the entire motherboard out of the case, so the cutout did not matter to me.
In any event, my next case will be the HAF-X because of the nice features.