I can't disagree with you, but against that, there's the plus of getting a slightly less restricted air flow. I know that any mods to the properly designed system are usually a bad idea, but one of the parameters the original designers had was quietness balanced against air flow.
Its pulling air from inside the engine bay, yes, but it is at the front and I am in Scotland, the ambient air up here is 6 degrees today, so I'm betting the air in the engine bay is a darn sight cooler than outside air in say, California!
Drilling out a spare airbox would be an option, too