When it is in "best for retina" mode, it's running at the "optimized" DPI mode that Apple thinks is the best for that display size, regardless of your preferences of how small / large you prefer things to be.
All the icons / UI elements, etc. were specifically designed for this DPI scaling mode....the other, higher scaled modes tax the fake intel GPU more, as they have to adjust the "optimized" UI elements and make them smaller and give you more screen real estate. More screen real estate = more pixels to drive = more mathematical calculations = more taxing on the fake intel GPU (OK it's more like an APU but it's still not a real GPU).
Again, Iris Pro could have fixed this in a heartbeat because of the dedicated 128 MB of eDRAM and Crystal Well design ( for more info about that and why the memory bandwidth of Iris Pro is so much better, read http://www.anandtech.com/show/6993/intel-iris-pro-5200-graphics-review-core-i749 50hq-tested/3 ) but for whatever reason, Apple chose not to include Iris Pro chips as an option for the 13" retina. I don't know why they made this decision.