Hmmm... I guess that's what happens when your chance of making sequels is dependent upon player or audience response: You suddenly find yourself given the opportunity to develop a new story, but in order for it to work, you have to contradict some of what you said earlier.
(a la Zephram Cochrane being from Alpha Centauri... until ST: First Contact, or Miles O'Brien being a lieutenant until Barclay has to give him an order... then he gets conveniently demoted to Chief Petty Officer.)
Actually, this is further off the topic, sorry, but... wasn't there a sort of implication in WC1 (in the Secret Missions... #2 if memory serves) that Halcyon actually commanded the Claw? Maybe I'm missing something here, but I had that feeling.
I'm ready to be told I'm completely wrong on this one and wouldn't be surprised. It's been a while since I've flown off the 'Claw.