I think part of this discussion is mixing up runtime dependencies with development dependencies. Most of the examples of non-Python tools on PyPI seem to be dev tools, not things used at runtime — and that’s an important difference.
For dev dependencies especially, the reality is that tools are written in all kinds of languages. If every ecosystem required those tools to be repackaged into its own format so they can be installed via its native dependency manager, that creates a lot of duplication and extra maintenance work — either for the original maintainers or for the community.
Several alternatives have been mentioned (Nix, Conda/pixi, curl | sh, go-to-wheel, etc.). Personally, I prefer relying on the ecosystem where a project officially publishes its tools, rather than on community ecosystems that rebuild and redistribute them. Linux distributions are a bit of a special case because they’re curated and maintained by stable teams.
One thing I’m surprised hasn’t come up is mise. It provides a unified CLI that can install tools from many native ecosystems, including tools like CMake or uv, and can even help with cases like Playwright by installing Node.js and then delegating to the native package manager. For dev environments, that kind of approach feels like a better fit to me than turning PyPI into a general binary storage platform.