One thing that gets me about the sandbox of flatpak is that it doesn't seem to be up to the user. If the developer of the app chooses the permissions, then there isn't a fundamental difference for security from having all permissions anyways.

Ideally a user installs the app and they would know, without reading anything else about the app, that the app is separate from their system. If any app you install is NOT separate from the system, then... the sandbox is like making a giant wall but having a door right in the middle of it.