I have Nextcloud running on a Raspberry PI along with a dozen other services on yunohost.org. Nextcloud automatically backs up my family's contacts, calendars, notes, tasks, photos, files, passwords, bookmarks, phone locations and more. If you want to backup the APK's check out Seedvault. I am personally fine manually reinstalling APK's if/when needed so have not tried Seedvault yet.

You need root to backup all app data:

Neo Backup - Currently maintained, and available on fdroid.

Titanium backup and restore - I don't think it is still maintained, but it still works.

Seedvault which does not require root can't backup a lot of things.

Depending on your phone, you may be able to backup everything with twrp, but it doesn't work with some new-ish phones.