Through trial and error, I figured out how to solve the problem.

Assuming it was a permissions problem, I first reset all the permissions to the ones all files had at the beginning. As expected, my conf file did not run.

I then copied the default dosbox configuration file from ~/.dosbox/dosbox-SVN.conf and edited that with my custom setup.

Now everything works fine, though I never did figure out which permissions were broken.

Thanks anyway!

@Efriim Batocera is very similar to Recalbox, since it was started by a former Recalbox team member - so I'd expect them to be very close.