Here is the advantage from my experience working with projects:
you can easily switch environments on a single nr instance
integrated git client
Got one node red flow.json for controlling heating, and another to control lights? Now you can switch back and forth between the two on the same machine with the same node red installation. Useful if you need it.
Git client, can be good, but may be a hassle. You can use separate repos per project, that's 1:1 and easy. But I really think the rest of the core files should be included too, like package.json and all the config files, settings.js ++. That'll be a separate "root" repo. You may or may not organize your nr project repos as submodules of that root repo. I did it, but sometimes regret it. Regardless, the root repo is outside node red so can't use git client here. All in all I think it may be just as good to just use git from command line, and/or a separate standalone client. But it certainly can be useful to have an easy git client available.