I see, so it's just a few mm, then. It could still work if you made it from two pieces so the GPU mounting bracket is recessed inside the back panel, basically forming part of the cutout or at least touching the I/O shield at the top, but it wouldn't be any interference, so to speak. Could make cooler selection quite sparse, though, even the NH-L9 (37mm from CPU IHS) would probably not fit below that, right?
Yeah the ones I know are dome head and a bit rough on the underside to prevent them from rattling free, that could be a reason.