I didn't think preferring to run in a virtual desktop would mean fullscreen was preferred... Not as much help on linux, but I used to have a virtual desktop fake fullscreen I do in Wineskin before RandR support was working... basically, change your main resolution down to the resolution you will run the game at, then start the game in the virtual desktop... on the Mac is easier cuz I can kill the window manager and it doesn't even look like a window, looks identical to fullscreen.... but it would at least be close on linux... the trick is to change your main OS resolution yourself first to match the game... not try to match the game to it.
