The first one allows Flatseal to edit the permissions of Flatpak apps including itself.
System folder access allows a app to read the filesystem. (But not system internals)
System settings access allows the app to change settings
So the only concerning one is Xournal. However, I happen to know that it doesn’t support XDG portals which is how apps ask for permissions to files so it needs full file access. As for the system settings I have no idea.