The original X-COM did not have the player equipping his soldiers at base, but rather stocking the craft before launch. With UFO: AI's emphasis on weapon skills, and greater emphasis on non-firearm equipment, arming soldiers at each deployment site would be too much of a hassle. Hence, soldiers are equipped at base before deploying, and it could be assumed that a PHALANX craft is carries some extra equipment stock for resupplies. Of course, this is not a literal mechanic now, more of an "oversight feature".
Perhaps down the road there could be an option to stock the dropship of choice with an extra load of equipment, which could be used to resupply troopers between multi-mission flights and for restocking or weapon switching on the battlefield.