https://html.spec.whatwg.org/#origin says:

If a Document was created as part of the processing for javascript: URLs

The origin is an alias to the origin of the active document of the browsing context being navigated when the navigate algorithm was invoked.

That seems wrong if the URL is targeted at a pre-existing browsing context that is not the browsing context from which it was initiated. The spec text would seem to me to give the document loaded for the javascript: URL the origin of the document that will be unloaded from the targeted browsing context.