Are you aware of flatseal?

If you are, is there an issue with using it for you?

I wish there was an option for an android style system where, when an application wants to use a permission for the first time, you get a pop up asking you to grant that permission.

Or, more generally, just some way to ensure that (a) a flatpak isn't granted the permissions it wants automatically and (b) I can then manually grant those permissions as conveniently as possible