There are cases with removable motherboard trays. Anyone tried finding a spare motherboard tray, or ordering one as a replacement part from a manufacturer, and using that to mount everything?
That, or you might be able to dremel out the rivets attaching the motherboard backplate to the rest of the box, and get the same result.
I'm going to try one of those two eventually, because my PC won't fit inside my arcade box while it's still in the case. (Everybody said "measure twice, cut once"... but did I listen?) At least that way, I get a nice set of screw holes that are already in the right places, and a place to screw down my PCI cards.