We dont live in such a perfect world. Linux has a small marketshare for non-server software, so packaging is done by your distro.
You would need to have user-facing settings for Apparmor or SELinux to replicate what already exists with Flatpak.
Principle of least privilege.
Maybe you prefer native packages, but bubblejail or SELinux confined users are complicated as hell and both are pre-alpha in my experience.
So yes you add bloat, dependencies etc. But you also add stability, a small core system, take load of OS developers and unify the packaging efforts so that it is done by developers not packagers.
This reduces complexity a lot, as the underlying system is not as important anymore, and you can just use whatever you want. Software is separated from the OS.