Did you calibrate Kodi overscan within the app?
Btw are you outputting over hdmi and composite? Why do you have other mode configs in place?
If you can't resolve it, you would be better reporting on the raspberry pi forums where you may get the attention of a dev.
Maybe something changes with the composite modes. If the terminal is fine, then adjusting Kodi display should work. If the terminal is also out, you can adjust overscan in config.txt.
If you don't use overscan in config.txt you should disable overscan and remove overscan_scale