How can I inform users about Flathub specific changes to my app like disabled/enabled features at compile time, tightened/loosened permissions, updated/added modules (e.g. for multimedia viewers new supported codecs etc.). Do I have to patch upstream’s AppStream data, adding items to the release description?
No, I don’t think that’s an information that matters to the users. The changes in the permissions should be handled by the application that will update the flatpak for the users, Flatpak CLI & GNOME Software already do that.
This would be really useful if it was somewhere accessible on the package download page.