Same here, I have yet to find a containerised application platform which fits my ideas of how to build a system. A sensible package manager with a reliable dependency graph - or plain old apt with judicious use of deborphan - goes a long way in allowing the installation of applications with a number of dependencies, testing it and removing all traces of it afterwards. Containers have their use but Flatpak and Appimage have not hit the right spot for me, at least not yet.