It's up to you, really, to only use flatpaks that declare tight permissions and implement the proper protocols to safely access resources they don't declare.
This isn't always easy and a lot of software on flathub is old-ish, so people tend to open up permissions since it's difficult to implement all these features properly. In my experience people will rarely stand in your way if you try to improve a package.
This isn't always easy and a lot of software on flathub is old-ish, so people tend to open up permissions since it's difficult to implement all these features properly. In my experience people will rarely stand in your way if you try to improve a package.