Regarding this issue using the FPS optimizer, I wasn't told this anywhere; Uncheck the 'novice' option and the ratio is available under the misc/2 tab.
Using FPS Optimizer to change the screen ratio and resolution will break things for MGEgui.exe (not sure about MGEXEgui.exe, but it's a possibility as well).
@Earthlinger
Assuming you are using the standard version of MGE, please post any MGE related questions in the http://www.gamesas.com/topic/1240985-morrowind-graphics-extender-mge/.
If you're using MGEXE, then you should post to the http://www.gamesas.com/topic/1340389-shelter-from-magnus-blaze-9/.