Modifying /flash/distroconfig.txt is the wrong approach - it will be replaced on every update. Commenting out the "include distroconfig.txt" in /flash/config.txt and replacing that with custom dtoverlay or other settings is even more dangerous as it could brick your installation on an upgrade - the stuff in distroconfig.txt is essential.
If you need to force a video mode you should add a video= parameter to /flash/cmdline.txt, eg video=HDMI-A-1:640x480M@60 - see the kernel docs for more info modedb default video mode support — The Linux Kernel documentation
It would help even more if you post why you need to change settings, which settings they are and provide pastekodi logs - then we would have a chance to look into it and if there's an issue we could fix it. If you don't report issue details and post logs they will never get fixed.
so long,
Hias
