You can keep install files to always be able to install a certain OS version again.
You can use tools like MyPhoneExplorer to easily backup and restore most of the user stuff including SMS, contacts and the whole so-called Internal Storage.
You can easily copy the Internal Storage via USB without additional tools.
You can install individual Apps again (even if this can be tedious if you use many Apps).
What you can’t cover this way is OS settings as well as Apps data and settings.
This stuff resides in the data partition, but not in Internal Storage, which is only a subdirectory on the data partition. Unless the phone is rooted, the user can’t access this part of the data partition.
TWRP is a way to get this stuff (by backing up the data partition), but in case of Fairphone 3/3+ needs keeping the bootloader unlocked to be able to boot TWRP when needed.
A rooted ADB shell is a way to get this stuff (doesn’t need a rooted phone, but the OS must implement Rooted Debugging, stable /e/OS builds might not do this, dev builds do) … a backup solution using this was explored here … [HOWTO] Backup and Restore Data on Android Devices - #36 by petefoth.
Otherwise you would have to explore data export/import options for individual Apps as well as set up the settings of the OS and your Apps again manually. Not nice, but having taken care of the other stuff is not nothing.