Flatpaks are not a secure sandbox. The sandbox exists to distribute apps, and the security is secondary. Apps are very minimally sandboxed. A better permission system would severely weaken the sandbox with basic permissions needed by so many apps. The amount of apps on Flathub that I have seen which need access to org.freedesktop.Flatpak which removes the sandbox. Browsers have their own sandbox crippled because Flatpak blocks namespace access, but that is not a problem for Snaps. Flatpak does not implement many (or any) modern exploit mitigations. Apps that have audio permission have microphone access, and access to all desktop audio. X11 access doesnt use something like Xephyr for a separate X11 to prevent apps from escaping the sandbox, especially on a X11 desktop environment. Etc, etc.

Now dont take me for a Snap shill. I don't think that is very good either. But at least its permission system is more thorough and apps tend to work better in a lot of cases. It also has on-screen permission requests (at least I think). It still suffers from many of the same problems as Flatpak.

I still use Flatpaks though. Just wish things were better.