I was able to analyze the issue a bit more yesterday.
Basically Vice is using this config file here: /batocera/system/configs/vice/sdl-vicerc
There are a couple of settings included for the video settings like:
Details about the parameters can be found here: https://vice-emu.sourceforge.io/vice_21.html
In any case, I would like to adjust the video settings globally as written in my first post above to change the border mode to Default (which means VICIIBorderMode=0) and additionally to keep the Aspect Ratio of 4:3 by setting SDLGLAspectMode=1.
When doing this and saving the file those two values ALWAYS get overwritten to the defaults. As @jackalpret already wrote, changing the settings for the C64 core won't make any difference.
Is this a bug?
By the way, I have already upgraded to 5.25.