Chris, Thanks. In fact, it is a bit difficult to know exactly which camera variables are affected by FoCal. It seems to me that FoCal sets up the camera, takes a shot and then restores the settings quickly afterwards.
One of the several things which Larry and I found we were "doing" differently was that he had his D800's picture control set to Neutral, whereas I had mine set to Standard - which causes a little more in-camera sharpening. Doing a direct NL vs SD test with a given setup is on my "to do" list, as well as running a test with sharpening set to zero...
Yes, FoCal uses only JPEG files and MAY even set the camera to generate only JPEG-fine.
If I can obtain a good, 77mm (or maybe a gelatin) primary green filter, I'll run a test to illustrate what you said.