Rye isn't aiming to replace apt. Rye is just aiming to do the same as Go, having one tool to manage dependencies. In current ecosystem there are many many different tools tho manage Python project's dependencies unfortunately.
We have been moving away from python packagers towards linux packagers because it is trivial to mirror them internally. We do this because external mirrors have been unreliable and we have full control over when updates get rolled out without having to pin every version (the mirror effectively pins them)