Don't mean to be a nerd but you're wrong.
You laptop will run cooler with the cover off than it would with the cover on.
With the cover on, the machine relies on radiation (and the occasional conduction if it's in direct contact with a cooler object) to dissipate heat; but with the cover off, it's all convection.
However, you are right about one thing, cutting holes in a laptop's cover is sure to disrupt the airflow scheme. However, this doesn't apply to the Macbook Pro as there isn't any significant inner to outer airflow. You see, heat dissipation with the cover on doesn't rely on any convection whatsoever.
Now besides all the physics, it's just common sense really ... You're exposing a hot object to a cooler ambient environment ... How can you argue that it will hinder the cooling? Lol?