Dont let this hold you back.
The backup tool is good for backing up a qube with its configuration in
a secure way.
But most of the time your concern is with the data, not the qube that
holds it.
You can run any of the tools you usually do, including borg. I use
zpagfranz for incremental backups,(against the snap volume for running
qubes), because I’m used to it, but you can use anything you like.
Optimally, use a disposable for the backups, and attach the relevant
volumes, rather than run anything in dom0. Or you can use syncthing to
keep data synced between your data producers/consumers and your backup
system.
Personally I tend not to worry about the templates or qube configuration
because my systems are fully salted, so I can recreate template and
qubes at will, but you may prefer to hold Qubes backups of those things
as snapshots, with incremental backups of the data.
Focus on the data and you’ll be fine.