Wouldn't the issue be negated to some degree depending on the placement of the option? Sufficiently "obscuring" the option would reduce the chances of clueless users from doing something they aren't supposed to. Even the options in right-click -> Properties rarely get abused, at least we don't get people randomly complaining about things like sync GPU thread or Projection Hacks. Of course it's not an idiot-proof option, but visibility sometimes makes all the difference between having idiots get to the option at all.
As for determining what settings to save, just use the settings that Dolphin already saves on exit (Dolphin.ini, gfx_opengl.ini, gfx_d11.ini). For all the other little settings (e.g. Projection Hacks, Speed Up Disc Transfer, etc), save them in the file only if they've been enabled through the GUI, if not pass it up when outputting the file.
As for determining what settings to save, just use the settings that Dolphin already saves on exit (Dolphin.ini, gfx_opengl.ini, gfx_d11.ini). For all the other little settings (e.g. Projection Hacks, Speed Up Disc Transfer, etc), save them in the file only if they've been enabled through the GUI, if not pass it up when outputting the file.