The 648x480 is a clever idea, it works with some emus, not all, but that's a good step forward.
Sega Supermodel, for instance, is trying to stick to a supported resolution, so it fallback to 640x480p, but i successfully tested a quick and dirty solution for that.
I'm launching the emu in 640x480 windowed mode and then center the window on the screen with a AHK script like this :
WinMove, Supermodel, ,-2, -25
In appearance there is no difference with fullscreen mode !
But there is still a big issue : i was mistaking when i saying that GMame was ok when using the right DVI output, my test was wrong (Gmame was not well configured when i reinstalled my OS)
It crashes, see attached "log3.txt"