That is correct. The best case is to write a script to make your desired changes, and then run it after each system update.
My own use-case is that I have a NFS mount-point for my Steam Deck to use extra storage on my NAS. After the first time I figured out how to get it mounted, I made a script to disable read-only filesystem, make all the changes to the system, and then re-enable read-only filesystem. After every system update, I just run that script once.