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This is one of the annoying issues with docker, or better, on how docker is abused in production.
The single instance/multiple databases is the correct way to go, docker approach mess up with that.
Rewriting docker files is always a possibility but honestly defies the reason why docker is used by self hosters.
Also beware that some devs will shunt you out of support if you do, specially the apps that ships docker files by default.
Go bare metal if possible, that way you have full control. Do docker for testing up stuff quickly and be flexible at cost of accepting how stuff is packaged by upstream
The official Postgres Docker image is geared towards single database per instance for several reasons - security through isolation and the ability to run different versions easily on the same server chief among them. The performance overhead is negligible.
And about devs not supporting custom installation methods, I'm more inclined to think it's for lack of time to support every individual native setup and just responding to tickets about their official one (which also is why Docker exists in the first place).