I'm going to say, that it is not cannon, precisely because the devs axed it.
They did not want that story told..(plenty of games have much longer intros, so its not about space)
If they did not want that story told, its not part of the universe, in my oppinion.
You know if you'd seen that the first time playing FL your jaw would hit the floor and you'd try blitzing through the game so you could get a nomad ship of your own (hell, I'd willingly commit murder just to get a chance to fire one shot with that supernova wep).
They might have dropped it cos of all the abuse they'd get for showing ships and weps you'll never be able to get (without modding of course).