Drivers. On MacOS they tend to be a bit behind the Windows versions, also MacOS itself is reasonably GPU-heavy. Add to that Apple's tendency to lag behind the latest (as in from the last five years) OpenGL standards and you've got a recipe for slow OpenGL.
Though interesting that it's an Iris Pro, MacOS used to have the best Intel drivers as Apple pulled them in-house. ATI and NVidia have always treated MacOS as a secondary target.
If it was a 10% performance hit, I could blame the driver but comparing 60 FPS (I presume) with 1 FPS when people are playing the game in Mac OS X using WINE; that sounds like something is probably not quite right in his code.
I also found that even with a GPU-heavy fullscreen application, having another (smaller) window on top doesn't noticibly degrade rendering performance. It seems the window manager is doing some clever things there in regards to compositing.
Though interesting that it's an Iris Pro, MacOS used to have the best Intel drivers as Apple pulled them in-house. ATI and NVidia have always treated MacOS as a secondary target.