I didn’t approach backups from this angle yet, so perhaps anybody else can answer this, hopefully.
I deliberately left my bootloader unlocked to be able to use TWRP, and since TWRP on the Fairphone 3/3+ for now regained the ability to decrypt user data (there was a period in which this failed), I’m basically back to doing what I described here in my /e/OS beginnings …
Additionally (or alternatively depending on how TWRP behaves) I’m using MyPhoneExplorer to cover things like SMS, contacts and calendar (and I let it do the necessary Internal Storage copy for me, too).
In case TWRP can not decrypt user data the backup problem not covered by other means from my point of view would be /data with the exception of /data/media (= Internal Storage).
I planned to have a look at ADB for this, because Rooted debugging is available in /e/OS’s Developer options, which would give root to ADB (without having to root the whole OS), which would give ADB access to the whole filesystem including /data … but then TWRP regained decrypting ability and I didn’t need to look into this yet.
I’ll just see whether TWRP can decrypt user data or not and apply my comments above accordingly.
Without TWRP able to decrypt, or with a locked bootloader and thus without TWRP, I guess using ADB with Rooted debugging would look most promising to me.
Seedvault, which is included in /e/OS, might be worth a look from Android 13 on, too, as I seem to remember that from Android 13 on this would not be “Apps have to opt in to let themselves be backed up by Seedvault” anymore, but more universal … but I would need to read up on that again myself.