To be honest, I think the IOA Dueling Dragons policy is more because the unload area is not in the same place as the load area. So you would have to walk back up the track to retrieve your shoes. That just begs disaster if somebody walks too close to the moving train and gets whacked in the head.
At Kraken, the load & unload is the same spot. So easier to retrieve shoes and no risk of getting in the way of the ride ops folks.
Also, I think Sea World is a little more laid back about their rides than IOA.. which is pretty rigid on it all.
=)