Quite a few years ago, when Flatpak was a brand new project, I met some of the original developers. I tried, and failed, to convince them to change one particular fundamental part of the design. In the original design, and today, an installed Flatpak has a name, the permissions are bound to that name, you run that Flatpak and it has its assigned permissions, and, if anything else talks to it, it talks to it by that name. If I install a VSCode Flatpak as my UID and grant it access to my Documents directory, then VSCode, running as me, has access to Documents.
I argued that this was the wrong design. If I install VSCode as me, then there should be an installed copy, and that should have approximately no significance. If I run VSCode, then the running instance should have some id (possibly ephemeral), and that instance should have a set of permissions. If I want to run VSCode with access to ~/project_a and another instance with access to ~/project_b, it should just work and the instances should not be able to access each other's data, even if they're running at the same time. If I want to run two Tailscales, it should work. If I want to fire up an ephemeral instance of Firefox, that should work, too.
However many years later, I still think I was right. Flatpak gets this wrong, MS and Apple's App Stores get this wrong, Mac OS gets this (very very) wrong, etc. There's plenty of opportunity to do better.
(This is important from a bug-mitigation perspective: a LibreOffice document that achieves RCE should not be able to access my other documents. It's also important frmo a vendor-doesn't-care-at-all perspective: VScode has basically no security to begin with, and VSCode inside Flatpak ought to have a degree of real security courtesy of Flatpak.)