It does not defeat the purpose. The place to customize your system on the system-level is /etc. By the way: Every time you update to the next image, a snapshot of your current /etc is taken, so that when you roll back, your /etc also rolls back. And if you really screw up, then you can still restore the current “original” files from /usr/etc.
This is great. I think I will create a structure in /root/customization/... and simply link to it.
For example , this can be: /root/customization/etc/systemd/system/fix-yoga-speakers.service
Then I will symlink /etc/systemd/system/fix-yoga-speakers.service to point to that file. This way I can have all my stuff in the root user’s home, in one folder.