The link you posted, while interesting, doesn't substantiate the claim that Python was "designed" to be glue code. It is a nice side effect due to its simple yet powerful syntax and extensibility using CPython.
That non-python dependencies being a problem is not surprising and I don't think any language has really solved that. C/C++ doesn't have a dependency system, no package or library registry nor manager, no universal build system, and no version manager. Building anything of that language alone is a chore. Rust has to be present on the system and in the right version. D, Zig, Go, and others too.
If you're on Linux there's a good chance the library you want to use is already compiled for you and you can just download it as part of the Python package installation. Building it on linux is peeking into Pandora's box. Building it on non-linux is opening Pandora's box. The only non FHS Linux I've encountered to solve the dependency problem somewhat is NixOS.
IMO to complain about non-python dependencies is born in ignorance of other build systems. If they can't solve their own problems, it's a tall order to demand it of Python's packaging system. Python isn't perfect, of course, but the problems we're talking about here aren't python problems, IMO.