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That's what I do. I always thought I was doing it "wrong" but it just made sense to me. I can also just up/down/etc... compose files to individually pull new images, test things, disable a service, and apply config updates without affecting another container at all.
I even keep my docker config files in a seperate directory so I can backup the docker composes in a second over the network.
I started by using a single mariaDB instance with multiple databases, but now I see the same benefits from moving to one database container per compose file that needs it to make it even more flexible so I don't need to start up mariadb and redis before all of my containers.
File permission problems? Down the compose that needs it, fix it, re-up it without losing any uptime for other services and never having to use docker commands kludged together.