Esam Plugging the key into the phone during the process of adding the key to Proton account doesn't lead to any reaction from proton! I can not activate the port temporarily by changing a setting to overcome this?
Practically most security key functionality on GrapheneOS requires Sandboxed Google Play. This is because GrapheneOS currently doesn't have native support for security keys (and neither does the Android Open Source Project, which GrapheneOS is based upon). (There is another app that adds support for this, but it currently doesn't work well for registration). Are you using Sandboxed Google Play? And which web browser are you using?
My understanding is that you're trying to register the security key when it's plugged in to the USB-C port. That should work with Sandboxed Google Play.