What is so different about the race course that it requires you to use something other than a mtb?
I think its tradition. Cross is been around many, many more years then MTBing has. It has its roots in Europe and its something the roadies did in the off season to stay in shape.
However, a cross bike has bigger gears so in theory on a cross course, the right cyclocrosser would stomp the right MTBeer only cause he could push a bigger gear and thus go faster in the flats and straights.