I use DivestOS which is based on LineageOS and these have SeedVault integrated in it as a backup solution, but since it doesn’t work well I’ll tell what I do (If your OS has Google’s backup solution, it works well to a certain extent, but there are times when it cannot restore things like call log/sms even though it backs them up).

• I backup apps, SMS/MMS and call logs with Swift Backup
  • Since I don’t have many applications, I examine each application one by one to see which data can be transferred and in what way.
  • I backup data of the apps like Aegis, NewPipe etc. to their respective Android/media folder, which means I basically export Aegis’ backup file into /storage/emulated/0/Android/media/com.beemdevelopment.aegis/backups, with this way, I can back up and restore the media along with the APK of the application using Swift Backup. If you find this step unnecessary/complicated, you can create a folder called Backups anywhere and put all your backup files there.
• I backup files and folders with Syncthing, it basically sync’s 2 directories between 2 devices and I sync all my folders into my PC with some ignore rules (for example, to avoid synchronizing the .thumbnails folder unnecessarily). Also if you stashed all your backups/exports into some folder, it will also sync.
• Technically there is no need for a non-APK backup for applications that have their own cloud based backup mechanism or are cloud-based.

When I take these backups, I can completely restore the phone to its previous state even after factory settings. Of course, for a cleaner start, sometimes I don’t sync some folders back or don’t reinstall some applications. To do this the way I want, I reinstall and restore data of the applications one by one.