First up, this is an enthusiast question. In the past, I have installed multiple desktop environments (DE) on Ubuntu and paid the price! Multiple programs for the same purpose, icon sets, funky window borders, uninstalling etc. But I thought that rebasing would resolve most of these issues. Yet this practice is still discouraged [1, 2]. In theory, I understand how different DE configs can mess up things. But if I assume no layering performed by the end user, only flatpak or homebrew installs, what are some reproducible examples of such issues that some of you have gone through?
So this means there exist common config files that are modified in conflicting ways by different DEs. Is this a universal statement for any two DEs, A and B? Or is the problem particularly acute for certain values such as A=GNOME and B=KDE and not so much for others e.g. A=GNOME and B=COSMIC?