The extended intro can be considered canon as long as people can elaborate further the lore. Since that doesn't happen, it should not. Though the extended cut can elaborate and direct further possibilities of the Nomad lore and such. It doesn't necessarily contradicts the FL campaign. It's only how you see it. Most people don't see it.
Also, as far as I remember, there was another ship that was sent as a test. Nobody ever heard about it ever. Would be cool to explore what happened to that.
Rudimentary creatures of blood and flesh, you touch my mind, fumbling in ignorance, incapable of understanding. - Sovereign