@Kerosene flatpak allows you to grant persistent file permissions. you can even edit them with flatseal if the packager goofed it or you just want it to be looser (good for losslesscut which is only allows like one folder by default)

so you can open up ~/.catblob/* to store scripts.

there's also some ability to define extension points which exist inside the bubblewrap. that was added for things like ardour, which relies on plugins for audio effects, so different flatpaks can bridge together if they are defined as plugins.