Yes, only crossing an external border count as an entry or exit and air travel is no different in this regard. Airports in the Schengen area have often been reorganised to process Schengen flights separately, typically with no official passport check and occasionally withsometimes no ID check of any kind (i.e. not even by the ground handling personnel). Airlines might still occasionally insist on seeing a visa but since you have one, it should not create any problem.