To add onto this, if you really wanted to rebase and don’t want config file clashes, you can use ostree config-diff after rebasing to show what config files changed. You can also simply remove all the files in /etc, and on the next boot, ostree will re-populate it with the contents of /usr/etc in a three way merge. Just be sure to copy, at bare minimum, /etc/shadow, /etc/passwd, and /etc/fstab otherwise it’ll be very awkward when you try to boot again and your boot process fails because it doesn’t automatically mount your disks and you can’t login because you have no users. It’s kinda cool tho, that, at least for this very specific issue, those 3 files might not be needed if/when systemd-homed’s JSON User Records and Discoverable Partitions see wider adoption.
(Note: this is dumb and error prone, and you should absolutely do what the other commenter said)