I’ve tried to combat this a bit with a global Flatpak override that takes unnecessarily broad permissions away by default, like filesystem=home, but apps could easily circumvent it by requesting permissions for specific subdirectories. This cat-and-mouse game could be fixed by allowing a recursive override, such as nofilesystem=home/*.
But even then, there is still the issue with D-Bus access, which is even more difficult to control …
I think it is sad that Flatpak finally provides the tool to restrict desktop apps in the same way that mobile apps have been restricted for a decade, but the implementation chooses to be insecure by default and only provides limited options to make it secure by default.
If only more Linux programs followed sandboxing best practices... (i.imgur.com)