Its a silly default. Might also be to allow people to edit /etc configs with the app since its a basic editor. With enough dummies complaining about “doesn’t work can’t access files in <directory>” the dev may have set that to reduce negative review bloat (seriously look at the flatpak and snap stores and the number of bad reviews due to people not understanding the permissions system).
I would be turning that off immediately until I knew how trustworthy the app was or not installing it, just saying I can see where that default setting might be coming from.
Flatpak could use a permissions prompting api, so a prompt could be displayed to the user when they try to access a file outside the permissions scope, but that’s probably a lot of work to get in place. Maybe something we’ll see in flatpak in a few years.
Until then I think there needs to be some way to point new users to Flatseal and a summary of what these warnings imply and how to grok them.