I think the mistake of modern JS (and many other languages) is conflating source files with libraries. A better model is combining many source files into one library file, which provides one toplevel name when imported. A good example is how Three.js, which has a complex internal structure, gets distributed as one file and provides one toplevel name THREE. And of course there are many examples in C-land, where a large library can live behind a single header file. A project should only depend on a handful of those, and there should be few dependencies between them, so package management becomes easy enough to do by hand - just drop a file in your project's vendor/ directory.
As a bonus, this fixes the problem of having many fine-grained imports. If done right, your project's source files might not need any import statements at all. Anything inside the project could be available without ceremony, as if it was all one big file, and external libraries live in a handful of big namespaces which are also available without ceremony.