Not to give them an excuse, but presumably they would need a decent sized staff to handle all exceptions of students coming and going. I could see process-wise how an organization just has their policies spelled out and it is what it is. My daughter and I have already ran into a couple of issues with BYU that just seem patently silly and that you can't get anyone to change their mind.
At alternative for your son may be to attend BYU SLC and BYU night classes, which you don't have to have regular admission to attend and then he can 'transfer in' with those credit hours?