Just like Android, you can control the access to system resources by Flatpak applications. By default, that happens with Flatpak commands and not everyone can be comfortable with it. And hence, there is this tiny utility called Flatseal that allows you to manage and control the Flatpak permissions at application level.
Note, this does not work with system/root level Flatpak apps.
If you have tons of Flatpak applications, you can see what permissions an application has and control those permissions with Flatseal. Here are more details.