I have configured manually dozens of servers, and automatically many thousands, with no significant issues. Only when you fight the distro, you’ll end up caught in an edge case. These things are tested automatically 24x7.
I mean on Linux you have the source and everything is debuggable but imagine 10 apps needing 10 versions of the same software. If it comes to this, it will be a fork moment except you can't fork freaking windows!! Stop trying to make windows Linux and Linux windows. They are both great for their uses, this childish war where one or the other needs to be the only way is silly. This silliness is how we have one browser to dictate everyones needs now.
Been using Linux for over a decade and haven't run into any problems from apt/repo's. So I am using what I believe to be a qualified opinion when I say edge case here.