Well, but I don't understand your second point. In a desktop you can choose the graphics card. So if you connect the monitor to the GTX 560 output, it doesn't matter which Intel HD graphics you have. You are only using the nvidia card. Thats the advantage of a desktop for us. Because in a notebook you can't choose the graphics card and you have to use the intel graphics too (nvidia optimus technology).
Your first point brings me to my recent thread about intel iris graphics. Maybe the higher resolution of the retina display makes the difference and not intel iris pro.
Can you connect the MBP to a FullHD monitor?