With adequate exhaust and positive air pressure, this shouldn't matter. I've got a 240mm rad(push/pull) as intake for x2 290X' and my mobo temp never exceeds 32 deg C
Only info missing here is the ambient temp..the relationship just seems to linear to be a case airflow issue. The GPU temp shouldn't get worse as it draws cooler air from the bottom.
It's preferable to use a GPU with a blower style fan in small cases that way hot air is blown out the back of the case. In your case the axial fans are throwing the hot air inside the case with inadeaquate exhaust.
Get a better case or change your GPU for blower-style cooler or install more exhaust fans.
There's only one I know but it's very pricey - PC-Doctor service centre.
That said, it's a case of elimination starting with the OS, then hardware...there isn't any easy route, too many factors that can contribute to the anomalies.
Sounds like a noisy bearing. You could try some WD40 (or similar) to grease it if the PSU is no longer in warranty and can't be returned/repaired.
I had the same problem with a new corsair PSU but sorted it with some lub (couldn't be bothered going through the RMA process.
Hmmm..my guess it they weren't as complex as those of today.
moreover, you are comparing a device specifically for one task to another that must perform very many (processes)
It might just be your case design.. fan meshes/cut-outs etc can cause turbulence creating noise amplified when fans spin up... i've used Noctua fans in a Aquila Xigmatek as exhaust...what a waste of money it was.