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 that problem - which also make it extremely simple to fix issues like the one you have with a single config file - led to the development of Flatpak and Snap. You can accept the solution or live with your own self-imposed limitation.

Some traditional mutable distros also ship with Flatpak + Flathub configured out of box and present the software alongside their own distro-specific packages - Linux Mint, PopOS, Clear Linux, CentOS, and Fedora Workstation come to mind.