Just my 10 cents, and not to take away from the helpful comments here on backups, but stepping back a bit: I’m really not sure if ‘synchronising’ installs of Discourse is worth much effort.
Unless you intend on PRing into Discourse core, developing plugins or TCs is where it’s at and gives you the most robust, efficient solution for customisation.
The key thing with developing Plugins and Theme Components is they will be deployed to multiple instances of Discourse over which you may not have control in any case?
So having a slightly unique local Discourse instance for development is totally ok. (within reason)
The key workflow should involve keeping the plugin or TC up to date in a shared repo, most likely on Github.