Of course it is. Someone who read your comment and didn't question it might now believe that Flatpaks would enforce filesystem sandboxing and prevent, say some game, from accessing their shell configuration or ssh keys. That's false and it's dangerous, because nothing is worse from a security perspective than misinformed users who have a false sense of security.

> but this sandboxing becomes useless on X11.

That's also false. For example X11 provides mechanisms like the X11 security extensions which prevent clients from accessing each others data through the X11 protocol (like key events or buffer content), which means when I run my color picker or xev in a such an X11 security context they literally stop working outside of their own window. Firejail makes this type of sandboxing easily accessible and it also provides the ability to easily isolate x11 clients with xpra or xephyr.

So it's not like it can't be done, it's just that Flatpak doesn't care about it -- which is fine. With dbus you get the same issues, because clients on the same bus aren't isolated from each other. In this instance however Flatpak cared and implemented a dbus proxy to isolate clients from each other without throwing dbus away.

I agree, but definitely not this way! The sandboxing details must be 100% controlled by the user. The people who distribute the application should have no say whatsoever about their required permissions. That's ultimately for the user to decide. From the point of view of the application, all files are visible, but it may be a mock filesystem with mock resources. Letting the application distributors chose the permissions defeats the whole purpose of the sandboxing.