I think you’ve gotten a really bad read of my article. We know the typical Linux stack has problems with libraries failing to maintain backward compatibility and even when they do, the guarantees are nowhere near as strong or long-lasting as on Windows.
The problem is ultimately cultural. My article is essentially an appeal to anyone willing and capable of building a sane userspace through a single distribution. If that distribution adopts the stack, others can copy it or diverge at their own cost.
As for separating the userspace from regular applications, the point is that the OS shouldn’t treat system packages and user packages as the same thing. That’s separation of concerns, not a contradiction.