And just to extend on Darius' comments, some MBP models can't handle a SATA III device in an optibay - it just won't even boot.
I regularly run VM's on an external drive via USB 3 - works just fine (especially with a SSD). So I'd go with your first config, and I absolutely would recommend the 16GB of RAM. The Retina also has a newer processor in it than the regular ones.
FWIW, Apple is expected to bump the retina MBP to the new Haswell processors soon...but soon could be anywhere from tomorrow to October.