Some apps, not familiar with all of yours, have backup software or can easily be scripted to have a full consistent back. In Nextcloud case, the Nextcloud manual tells you how to do a consistent backup. So, in my case, I back it up from within the container via a shell script. In other apps like Emby, the software comes with backup software. I just use it.
Another way that is easier is to (likely script again) shut down all apps, take backup, start them up. Or an app at a time if you wish. Pretty much guaranteed good consistent backup.
I’m sure there are other ways as well. Off the top of my head.
Personally having a lot of service running i rely most on replication of volumes. Also (but not so often) i copy folders and files via SMB to an external disks (2 click with free file sync).
Managing stacks with Portainer i have also all YAML into his native backup + a private GitHub repository
Replication will not give consistent backups depending on how you set things up. Nextcloud for example has a very specific sequence to get a consistent backup, and, if you don’t have all pieces in one stack, they may depend on each other. But it is ok in most cases.