Maybe Jon can answer personally on this, but I think listing in order of preference makes it more difficult to fill the order, which is why Jon asks for it to be listed in numerical order. If your alternate list is also in numerical order, then after he goes through your primary list, he can go through the alternate list to fill how ever many was missed from the primary.
Consider that your primary list has several that could not be filled due to high demand, so that he had to take many from your alternate that was not in numerical order. It would make your order much harder to fill and could result in it being delayed.