The sad thing is that we've had a solution to this for decades. Installing Mastodon should be "apt install mastodon" and you're done. Maybe add a PPA first if it's new enough the distributions haven't included it yet.
But people keep using Docker for this. The problem is that most users, even many sysadmins, have never used Docker before. Then they look into what it is and discover that it's a heavy, complicated thing with security issues and the user walks away.
I mostly blame the UX the package managers have for package maintainers for this. It needs to be as easy to create a package for the major distributions as a Docker container. Otherwise people take what looks like the path of least resistance at first and then don't revisit the decision soon enough.