I think that may depend on the kind of changes you want to make. As a concrete example, on stock Debian stable, uninstalling LibreOffice and then updating and

I think that may depend on the kind of changes you want to make. As a concrete example, on stock Debian stable, uninstalling LibreOffice and then updating and upgrading will result in the package manager cheerfully offering to uninstall most of the Gnome desktop. This is because of LibreOffice being a dependency of the gnome-desktop meta-package. There are ways around it. My personal experience is that if I stay with the default desktop packages and just add things I need, the stability is quite good.