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.
They are not the same things. The App Store Wireguard does not support certain directives that are included in the CLI version (see my comment further up the thread).
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).