At the very least, Linux package managers should have some concept of different layers of packages.
For example, there might be layers for “system” (core components), “environment” (display manager, DE, etc), and “user”, each of which are maintained fully separately so they can’t ever step on each others’ toes and break things. Yes, it means there will be some redundancy but for all the trouble and complexity it’s saving I think it’s a worthwhile tradeoff.
Most "immutable" distro flavors do something like this. Back when I ran Aurora, it was rpm-ostree for the core system packages and homebrew in a devbox container for the rest. One incentive for maintaining the layer separation was that rpm-ostree was slow.
I've since moved my desktop box to NixOS, where everything is just flakes, but my mac runs circles around it so it's just there for Steam nowadays.