If that's the case then the GUI app isn't open source and is a completely different product from the CLI version, and differently licensed. If the CLI version can't do everything the GUI version can, I'd be keen to move to a more open and honest platform, especially for something as personal as a VPN.
Note that the command line interface for Wireguard is not optional on the server, the Wireguard App on the App Store is not sufficient for managing a Wireguard server due to macOS’s sandbox restrictions. (Specifically, the PostUp and PostDown directives are not supported in the App Store’s Wireguard App).