Joe was probably designed with High Composure. If I were a designer I would have the ability "Pocket Presence" give a ratings boost to accuracy while standing still but a heavy negative while trying to throw on the run, hence the speed and agility hit. For all we know while throwing on the run it probably factors agility into overall accuracy of the throw ex: (agility + pass accuracy)/2 = Scrambling Pass Accuracy. Someone could test this by giving a QB Zero agility rating and see how he throws on the run with and without Scramble ability.
Pocket Presence could also just represent the play style of the QB and not infer any bonuses. (Drew Bledsoe the Human Statue)
As for the pocket collapse/ composure rating I would represent it with the Clutch Ability. Did Marino have Clutch ability assigned? Then again he was probably designed with lower composure.