There are these setting in the setup.ini file in the GG root folder or the reloaded folder.
fullscreen=0
width=-1
height=-1
Maybe messing with these will give you the results you need. Not sure if this is just for the editor or just build game. Right now I noticed that if the editor is not full screen, then picking objects for editing is difficult as the mouse wants to sense the object about 8ft away form the intended pick object. So might not be fully implemented yet. But might be worth a try for test game and build game.
Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz, 2400 Mhz, 4 Core(s), 4 Logical Processor(s), 8gb RAM, Nvidia gtx660, Windows 7 Pro 64bit