In a way, it's been superseded by create-react-app and it's ilk, but I think those kind of tools are fine. If you're reaching for a tool like create-*-app, then you've already made a specific choice about a number of things, and it's just helping you to bootstrap the project.
It going to happen again soon with WASM. But I'm welcoming that. We'll probably all end up writing full stack Ruby, or something.
And in the case of setup tools, they tend to all suffer from the problem of being very difficult to change once setup. The tool you use to build the customized foundation is often unable to make future modifications if you have changed any of the generated code.
But by now we know the 99% common options people want: a choice of a few databases, (probably but optional) user profiles and auth, etc. The database side is pretty much solved, but the user management is definitely not - and it's the source of so many data leaks.
Not sure if Yeoman is still around but did they not attempt something similar?