Why is it that my MacBook Pro Retina's resolution is detected as different based on the application?
I am an iOS developer, so have a bit of an idea what is causing this.  Apple measure screen size in points rather than pixels, and depending on whether your screen is a retina display or not, will change the scaling factor between points and physical pixels.

In your case, because you have a high-resolution Retina display, OS X is applying a scale factor of 2.0.  This means that a webpage that has been designed with an element 500px across will still appear the right physical size (however it will in fact be 1000px across).

It's not a bug, it's a feature that means the retina display can still show the "old-fashioned" normal resolution content.