The idea is that you tinker with the system tree as little as possible, to avoid creating dependency issues or stability problems.
That's one for the "Linux never breaks", but anyway.
You still can install native packages on the system tree by doing an operation called layering. But you should keep it to a minimum. I personally create layers for system codecs or modules and a few exceptions where the Flatpak ("the canonical way of installing apps") is not really working for me.