yes, you're new to batocera ;-)
batocera architecture is really different. the system is more like a firmware.
system files are unmodifiable technically. unbreakable. and the whole system is only one file. cleaner to upgrade.
ok, of course, as you've seen, you can modify it. it's because we use a linux feature to that, allowing to write on a read only file system like a cdrom or a firmware. It's like a tracing paper on the system. this paper is saved in memory. thus, when you reboot, you loose all. as if you've never modified the system. more clean. it's why reinstalling batocera is useless, and it's why you can change from batocera 5.17 to 5.16 to 5.17 again so easyly. in case you upgraded and that you want to roll back to the previous version.
ok, but you really want to modify the system ? yes it's possible too. modify it. then, call the script /recalbox/scripts/recalbox-saveoverlay.sh to save the tracing paper on a file. this paper will be reapplied at each reboot, but lost when you will upgrade (i remove it because these paper are supposed to be for debug purpose only).