This is one reason I increasingly don't like the normal Linux distro "system packages, plus everything else under the sun, with one interface and all co-mingled" default package management solution. I big fat "update the system" (or don't) button with my user-installed packages totally separate, as I get with macOS, is nicer. This made worse because, unless you're self-managing the base system and keeping it super minimal (as one might in Gentoo, Arch, or Void) Linux installations are weirdly fragile, I think in part because of this too-large package ecosystem all tied up with the "core" of the OS.
Especially on a single-user system, I should be able to install most software without escalating privileges. I should be able to blanket-update my user-facing software without any risk whatsoever that a kernel update will get thrown in with that (even if I don't read over the list to check—it shouldn't even be possible), nor with privileges to perform such even if it somehow did try to sneak in. I ought to be able to delete the directory with my user-installed packages and the system still boots with no errors or warnings—and yes, with a GUI and audio and networking and all that still working.
I know Nix and even a Homebrew port (with worse package availability, though) are options for achieving something kinda like this but it still feels like swimming against the current.