It wouldn't be hard to display "remove configuration and cache files?" modal during uninstall/trashing process. But it would be hard to go against own simplicity of platform usage idea - that's the problem.

KDE's Discover after you uninstall a flatpak application shows small infobar (still really easy to miss) saying "appname is not installed but it still has data present." with "Delete settings and user data" button.

But then, all sort of software even on Windows leaves some kind of traces of own presence.

In a perfect world we'd have a standardized application uninstall procedure - either by dropping icon on trash (which is something still many people do - especially on Windows) or by bringing similar to mobile solution with "x" on longer click. All of this controllable by options for advanced users including optional configuration and cache files removal.