After some messing around, I found that the issue I was encountering when toggling the Arbitrary Limiters appears to extend to many, if not all, graphics settings when changed from the main menu, including the resolution (which I thought was working properly at first). I can change some of these settings by editing MainSettings.sav with a hex editor and the changes seem to stick, which leads me to believe that the game is not writing any changes to that file.
Some graphics settings are present in the character save files (maybe just the ones that are different from the default values, i.e. the ones that I changed?) but it may be preferable if they were saved exclusively in MainSettings.sav.