It is conceivable that it's different in the US, but in my experience in the UK, routine application processing may be done by administrators who might just be rule-following but nevertheless there is a responsible academic who goes by a title like Undergraduate Admissions Tutor. In a case where someone has an unusual background that may need to be looked at carefully, I'd recommend writing an email to that person, preferably before putting in the application. They can advise on what info to put where, or if necessary simply fish out the application before it gets wrongly dealt with by a bureaucracy it doesn't fit. I feel fairly confident that here, that would ensure that a strong candidate didn't get accidentally rejected for this kind of reason.
