I just replaced my 17″ MBP with a brand new 15″ rMBP. I still need to do a lot of Windows work, therefore I have Windows 8.1 installed (bootcamp and parallels).
I use my external Thunderbolt display at native resolution with the lowest scaling.
However I am not able to have both displays deliver crisp images. Either the built in display is blurry or the external Thunderbolt display is blurry.
The best setup I have found so far is:
Enable 'Let me choose one scaling level for all my displays' and set the size to 'Smaller - 100%'. Now the Thunderbolt displays works as it should. However everything is now waaaaay to small in the built in MBP Screen. I then switch the resolution to 1920x1200 and now items display at an acceptable size, however they are a bit blurry.
This is an alternate setup (rMBP display is fine here, but not the Thunderbolt display): Disable 'Let me choose one scaling level for all my displays' and choose the recommended size. Now things look great on the built in display. However the Thunderbolt display is now a bit blurry, because things are scaled up when they should not be.