> The "problem", in the sense that it's a problem, is that these languages and related technologies are all pretty good!
Yes; and frankly the development ecosystem for making software for linux & friends on top of apt/etc is terrible - at least from the perspective of a modern professional software engineer. The assumption is C, and C programs have no package manager - so of course dependencies get bundled / vendored sometimes when the alternative is linking to potentially out of date dependencies in apt. Autoconf/automake is awful to learn and understand. CMake is better - but its horrendously complicated because it tries to solve the impossible job of paving over all the junky custom compilation scripts that came before. (And it still has no cargo equivalent for actually fetching your deps.)
And then to work around all of that, each distribution will make weird, custom, maybe buggy patches to your software before adding it to their package managers. (Which has caused some high profile bugs and security issues a number of times.) Now when there's a bug, nobody knows who's fault it is!
This worked in a world when there wasn't much software, when releases were rare and when most programs only had one or two dependencies. None of these properties are true any more.
Rust, go, python and nodejs don't fit well with linux's package managers. The obvious alternative would be putting every crate, gem, pip package and npm package into apt, rpm and all the rest. And keeping them up to date with every version. But lets be real - that would be horrible. Apt et al aren't (currently) up to the task. (Can you imagine every npm package needing a maintainer in apt alone? I can just imagine the github issues: "I'm in debian stable and this transitive dep you're using only has version 0.1 available, from 6 years ago. What do I do?". Yikes.)
I'm sympathetic to the argument that modern million dependency software development has its own problems; but right now it (sadly) has no competition in terms of ergonomics and build reliability.