I would not worry about it. It is designed to run in clamshell mode.
I would think that a notebook computer is designed to run with the built-in monitor open and operating, that is why it's there. The design of the notebook includes that screen.
But, by that same logic, it is also designed to allow for an external monitor to be connected, and since Apple's current line of monitors are so much bigger than the notebook's screen, I would think the design is to use that one instead when available (when you are at your desk) with the clamshell closed. Doesn't make much sense to have a 13 or 15 inch screen next to a 27 inch one as part of the same work space.