I watched it twice the last few days. Half way through the Flood captures Burgundy and take her to the engine room to throw her into what looked like a Proto Gravemind. If the Flood wanted to learn to pilot a pelican why not just infect on the pel's off ramp and then have her turn around and pilot it to the Red Horse? Why take the long convoluted route. Surely combat form infection is good enough to pilot a vehicle.
That being said whatever happened to that Pelican. It was a good movie but the Flood acted really weird in it. Also no spore infections? Nani?