In regards to sandboxing, it only gets as far in the way as you ask it to. For applications that you’re not planning on putting on FlatHub anyway you can be just as open as you want to be, i.e. just adding / - or host as it’s called - as read-write to the app. (OpenMW still does that as we had some issues with the data extraction for original Morrowind install media)

If you do want to sandbox though, users are able to poke just as many holes as they want - or add their own restrictions atop whatever sandboxing you set up for the application. Flatpak itself has the flatpak override tool for this, or there’s graphical UIs like flatseal and the KDE control center module…