Remember, the sink full of water in my example is fully vented, and the air pocket still gets traped in the cup. The vent doesn't matter in this issue. It is the seal rings on your dip stick that is most likely causing thatlittle air pocket getting trapped in your dip stick tube. They seal so well that it traps air just in the tube, not the whole rear case. Its normal. Some dipsticks seal better then others.
Your trans/hydraulic system on your tractor does have a vent. On my kubota b tractors itwas on the right side, on top of the rear case, just under the seat. It looked like a rubber, black, candy cane top, you know with the little curl at the top. That was the vent, atleast on mine. Yours may be different, but should be located near the same location, either left or right under the seat comming out top of rear case of tractor.