You fix that by not using gnome. Or butchering gnome with enough extensions to functionally be a reverse lobotomy.
Since gnomes entirely shitck is that you don’t get to decide how gnome works. It’s out of the box or fuck off.
It’s why it needs a billion extension and mods to be remotely functional



Literally every distro ever even Debian. Has broken user space on updates. It just happens. It’s a fact of life. If your distro hasnt done it to you at least once you are either very new to Linux or you are lying though your teeth.