The typical "cheater" method to this sort of thing would be to just create the effect bright enough that you don't see the ship model spawn next to it as close as you can get it.
If you look very carefully at that video clip you'll notice the ships don't come into view untill they're closer to the camera or out of the brightness of the effect. They just make sure that as it's coming into view it follows a trajectory that makes you believe it came out of the effect without you actually seeing it happen.