It is a (faceless, but with menubar icon/menu) GUI app. It just happens to be automatically launched as an agent, both to ensure it's there for everyone, and to keep it running. It isn't automated, more than any other program is, and it's there to interact with (included activating and deactivating) the extension, as is required by Apple's design. And all that is done in a GUI context, which causes user interaction if necessary. (The only weird thing we're doing is, as part of the postinstall script, using launchctl bootstrap to get it running for all currently-logged in users. As is documented.)
And none of that answers my question, which was whether or not SysPrefs being launched on a resigned console was expected behaviour or not.