simple: AT tranny is bigger than the MT tranny.
because the MT is smaller, it creates a space for the MT AEM shortram to extend down into. The AT tranny is bigger and takes up more space so the AEM can't extend down as far, that's why they have a shorter one. they are the same price if i'm not mistaken, which is probably a waste of money since it acts the same as the $30 intakes you get off ebay.