Well, ideally the way it would be is "If you shoot it down... good, here's your XP reward for the mission!" If you don't it's "Oh shit, Koller has to shoot it down like the ruthless bastard he is!" As far as the civilians inside? Not the same group as the Easy Company civilians. The way the timeline would work is: Apollo Security Team shoots them down. Passengers die/are infested. Alpha Company finds civilians in Nakagawa Bay and bring them to the Delta Transport. Easy Company finds the survivors brought by Alpha Company earlier and leads them to the truck. Though that was my original thought if I remember Priyanka was already in the Delta Transport during Alpha Company. So maybe that's bust.