The module syntax inconsistency situation is atrocious but we're gradually making the transition. Now that we have a clear destination, I suspect it will be a non-issue in a few years. Projects like Deno and Pika are accelerating/papering-over the transition.

I've been working in JS for years and I've never encountered a module containing a typescript file with a .js extension... That was extraordinarily unfortunate. I don't think I've encountered a module containing Typescript at all. Correct practice is to build to JS and include the optional type declaration files. In my experience people are pretty good about that.