How about this suggestion.
Go with the base 2.3GHz with 256GB Flash Drive but upgrade the RAM to 16GB. I'm sure you already know that the Retina is not user upgradeable.
Going 16GB of RAM is a good idea since programs and OS's tend to get memory hogs when they get upgraded or updated.
Storage wise, you can always get an external drive which you can use to save your files to. Which is also a good idea in case something goes wrong with your Flash Drive that you have to do a reinstall.