You’ve decided that it has to be the traditional distro package manager providing the solution - but that isn’t going to happen, because those have been designed to manage a single installation of interdependent software with no distinction made between core system libraries or services and end-user applications. The solutions to the problems that come from that - which also make it extremely simple to fix issues like the one you have using a single config file - led to the development of Flatpak and Snap.

Some traditional mutable distros also ship with Flatpak + Flathub configured out of box and present them alongside and with equal importance to their own distro-specific packages - e.g. Linux Mint, PopOS, Clear Linux, CentOS, and Fedora Workstation. And Ubuntu is pushing Snap. So they’re all unlikely to start putting work into enhancing their distro package managers to start providing the desktop software specific features that you want.