I think most of the confusion here comes from the fact that there are two repositories:
One that contains the ruby + emberjs code - the canonical Discourse codebase. I’m assuming this is what you’re running when you’re talking about development environments. For development in discourse or on plugins, it’s faster and easier to work from here.
Then there’s the official discourse install that’s used for site deployments, through docker. The app.yml file is one of those, in common installs taken from the samples/standalone.yml template. It’s a convenient wrapper for docker that allows for easy deployment and configuration.
Backups - The app.yml file should also be backed up as that is your install’s configuration, which includes plugin details and email credentials. Other than that, the only thing you should need is the backup tar.
Before I waste my breath leading you down the wrong path, I’d be curious to know what you’re using a dev install for, as I would recommend staying away from maintaining a fork - If it’s to develop your own plugins, then keep on trucking with a dev env! If it’s to test out updates or develop themes, you can do that with a mirrored environment deployed under docker, in the exact same way that your production is.