Air bubbles...sure. That would make sense on a cross-flow radiator where the trans cooler is vertical in the "cool" tank. Wouldn't make any difference on a downflow radiator, where the trans cooler would be horizontal in the bottom (cool) tank.
The cooler is more-efficient (by something like 10%) when the hot trans fluid is moving in the opposite direction to the cooling fluid.
The trans fluid being cooled is moving "up" against the flow of the engine coolant that's moving generally "down" in that cross-flow radiator tank.
On down-flow radiators, the cooled fluid in the bottom tank again moves opposite to the engine coolant.
Either way, the "hot" trans fluid goes into the cooler port closest to the lower radiator hose (the outlet for the engine coolant) with the "cooled" trans fluid farther from the lower radiator hose.
