Makes sense to me. The air filter obstructs the flow of air, even if it's brand new, so there's always a little underpressure in the bellows no matter what. Opening the throttle increases air flow into the engine, and increases the pressure differential across the air filter: bigger air flow across the filter -> bigger differential. Since the air is sucked past the filter, the pressure past the filter -- in the bellows -- is always a tad lower. Manifold vacuum is a yet different beast -- basically speaking throttle body is just another obstruction. So you have two "vacuums":

no underpressure ==> air filter (small obstruction) ==> low underpressure
==> throttle body (big obstruction) ==> big underpressure ==> suckers (cylinders)

;]

Cheers, Kuba