I would put the covers on and take off the batteries only to remove weight from the rack as most hitch racks don't go to the weight needed to carry your bike. As someone who has the same bike I would not mount it with batteries but I also wouldn't worry about the batteries unless they are in a place to get easily damaged. Bosch batteries are pretty much the only batteries I wouldn't worry about all in a car unless it were a super duper hot car and the batteries were directly in the sun on the dashboard which is an odd situation.

If I was really worried I would leave them in a waterproof stuff sack so no air can get in. But I really wouldn't worry. Bosch has one of if not the best BMS' on the market.