From what I've tested so far, the only thing I've noticed has any effect on the whining noise being there or not are those two BIOS settings I mentioned above. The noise is there even with the bare minimum components required to make the PC boot, I even disconnected the CPU cooler's fan since I read someone talking about the possibility of a noise like this coming from low fan speeds or something. I've tested it in and out of the case, several cares, several power supplies, 1 stick of RAM in every slot, 2 sticks of RAM, with or without storage drives,different SATA ports, different outlets, different power cables, etc.
I also updated to the latest 3504 BIOS that just came out, no difference.
Of course, the GPU has so much coil whine, which just makes this even worse. I feel like I should RMA the GPU now, if that doesn't change anything, I need a new mobo. Or I need to get my hands on another GPU and test that first...
Edit: And I don't feel like disabling a bunch of features of the products I have just to circumvent some fault in them. I could test that just to see what it does, but it's not a solution. And same goes for buying extra stuff, I might as well replace the board, but that I don't want to do either when it still has over a year of warranty left.