I obviously can't know what he's thinking, but I wouldn't be surprised if that was part of his strategy to play to his cardio advantage. With a looser top control, he forces/allows his opponent to expend energy scrambling up, after which he's just going to make them expend more energy defending another takedown, and then scramble up from that one, again and again, rinse and repeat until his opponent is spent.
JDS was successful in fighting off takedowns and getting back to his feet for the most part in the first round, but how long can you keep that up against constant pressure before you just fold? For JDS, it was basically one round.
Compare this to what would happen if he employed perfect, ideal BJJ ground control principles. Well, he'd get one takedown, hold the guy down, maybe advance to a dominant position, hold that position...ok that's great and all, but such a BJJ attack necessarily slows the pace down. If the opponent makes it to the second round, he's still going to be relatively fresh, and ready to try to knock your block off again when the bell rings. The kind of pace Cain is known for setting is only possible with imperfect ground control...if he took people down once and they couldn't get back up again, his fights would look like GSP fights.
