Disable Opening Apps
The qubes-gnome-software-plugin plugin removes the ability to launch apps from Gnome Software, as a mitigation for opening software with internet connection, in templates.
Previously, in Qubes templates applications were opened without internet connection. However, when integrating Gnome Software with Qubes, it needed access to the updates proxy for Flatpak support, causing it to pass the proxy configurations to each app and open them with internet connection.
The image below shows what this solution looks like from the user perspective: