Put an exit at the top of /usr/pluto/bin/XConfigure.sh and it won't touch the conf file.
You've touched on a HUGE issue. nVidia's EDID support is all screwed up. To make matters worse, most TV's give wrong EDID information anyway, reporting via edid to use pc resolutions like 1024x768, not tv resolutions like 1920x1080. The reason is ce devices connected to tv's generally don't use edid; they just output 720p, 1080i, or whatever the user sets it to. Therefore tv's generally don't bother implemeting the edid information.
That's why by default the driver is told to ignore edid. Because in general when edid support is turned on, nVidia will switch to a pc resolution that the tv says it wants (like 1024x768), and then the tv can't display it, or displays it wrong, because what it really needs is 1280x720.
To really screw things up, around about December, nVidia fixed a major bug in their drivers causing crashes, but the ignore edid stopped working reliably. Some guys at Pluto found a work around (forgot what it is), which i incorporated in linuxmce, and for me it's now working all the time. But it seems this work around doesn't always work in every case.