Versioning is not the problem with package managers. It's entirely possible to implement a package manager that makes the right choices without changing how we version things. Cargo (Rust's package manager) does just that. That's why I don't think it's necessary to discuss versioning in an article about building a better package manager. Nothing interesting is trivial. That's almost tautological. Calling something out for being non-trivial is either meaningless or equivalent to calling it hard[er than it should be]. In fact, You don't actually need to make the versioning argument at all. I think you can make the exact same point made in the 3 paragraphs following my quote with the following single sentence: "By making the major version number part of the package name and combining the minor and patch numbers, we get a versioning system where the user is forced to pick a major version and can expect to always use the latest patch to that version". There are practical reasons why I disagree with the sentence above, but I think it does a pretty good job of making the same point you made in your article in less than half as many words.I'm talking about creating a package manager from scratch (I'm not proposing every package manager break their users in a post about not breaking your users) for some hypothetical next big language, and in that situation it seems worth fixing even if it's not that big a deal.
If this was the only sentence-level criticism you could make I'm not doing so bad :) Notice that I said "non-trivial", not "hard".