If you're referring to the hole just above the lip that's above the PSU mounting location, it's to route the front panel audio and USB/buttons for the case. You would need to be careful/delicate with the cables, whereby you had them laid first before dropping the motherboard in.
If you had an matx motherboard, that cutout wouldn't be covered up. The cost of tooling to punch that hole out on an atx case doesn't cost much so they do it regardless of you wanting to put an atx or smaller motherboard. To note, the case does allow installation of mitx, matx and atx motherboards.
If you're referring to the top right hand corner,
same practice applies, router wires first then drop in hardware. ^ Yes that's a build I got sponsored by Corsair to do. The
album to that build is here.