personally i think they're full of shit and are picking on u for some reason, it looks neat and doesnt go through anything major like the chasis rai,l u would have to be stupid to put it there lol
and the other side has two holes dirilled in roughly the same area, and prolly one isnt being used. but if you are running the standard plenum u can route your piping another way,
but then you make the pipes slightly longer..
hope i helped