Why would I want to use Babel to compile server side code rather than just use the latest version of Node? It's actually doing two compilation steps because it's got TypeScript in there too, which is also a compiler. It uses Jest for testing, which is primarily designed for React.
I haven't found my preferred environment scaffolding yet. As I go I find better and better ways to set up my app and usually it's pretty app specific. If I did find a great scaffolding tool I think it would be one I have full control over. Maybe a lot more like Yeoman which has been around for quite a while.
You can do a lot even without scaffolding, just npm init and git init.
I also find it's faster and has better features than Mocha (for instance, coverage out of the box).
This is meant as a simplified project build tool, not for every use, but you can configure it quite extensively if you need to (although it has limitations). I would estimation that ~80% of projects could use this, and is less than 5 minutes of migration or 30 seconds to get started. It's not for the 20% of projects with very custom needs for build configuration.
Basically it's a lego-like version of yeoman, and opinionated towards simplicity.
It's basically making a custom entry for that specific command and adding it as a bin in the package.json.