Everybody should do what they are comfortable with. In my experience transmissions don't suck water like axles because they have much less air and much more hot metal inside. A bit like the transfer case which also isn't a big deal.No its not because, again, four of the early TJ transmissions have vent openings that are lower than that.
22" or 30" or just over the hood I think checking all your fluids after you play in the water is a good idea, especially diffs, transfer case and transmission.