As a sandboxed app format, Flatpak apps have to request individual permission to access different parts of your system or your configured hardware. e.g., permission to access the network, permission to show notifications, permission to read files in you ~/Downloads folder.
As of GNOME 3.32 it’s possible to manage Flatpak app permissions on a per-app basis using the “Applications” section in System Settings.
Flatseal offers very similar features to those natively available, but within a slightly more efficient overview.
See Flatseal Makes it Easy to Manage Flatpak Permissions - OMG! Ubuntu!
Flatseal is a GUI app that makes it easy to manage Flatpak app permissions on a per-app basis. Free software, Flatseal is available to install from Flathub.