I driven many, many, many trailer miles all over the US both professionally and personally. For a good many of these miles, I’ve had a camera in the trailer to be able to observe and I’ve found that about 99% of the time, they haul better (esp long hauls) loose in a box. I’ve never noticed them having more trouble balancing. What configuration I saw that seemed the most stressful as far as balancing was a big 4H head to head and it was the horses in the back to straight stalls.