Of course, disabling xsettingsd returns everything back to defaults, but this is solved with literally a couple of commands or clicks with dconf-editor. It’s as if you install the desktop from scratch and customize it to your liking.
I just can’t understand why such different settings are used for debian and fedora (where GSD is the default)
It’s not just a couple of clicks if you have 50 different Debian qubes you need to fix.
The files you linked were added in 2015, maybe it made more sense back then.
I agree that this will be harder to do on templates that are already running. To be honest, the debian template as a whole seemed to me to be a mess of different packages and configuration files that conflict with each other. And this is much harder to solve than the fedora template.