While it may be true that the CARB certified, or Executive Order exempt, CAT's don't perform any better than the 48-49 state versions, there is something else to consider. After reading through the Executive Order that Walker/Tenneco has for it CARB-marked products, I read that in order to get that stamp, the manufacturer must give a 5-year warranty. Contrast that with the warranty on non-CA units. When I did, I saw that in the case of Magnaflo, they only gave a 25,000 mile limited warranty. That probably equates to about 2-2 1/2 years for the average driver. It looks like Magnaflo does offer extended warranties, though surely not for nothing. So while the CA catalytic converters may not do much more with the exhaust, they do get you a better warranty.
It may well be that the main difference between 50-state and 48-49-state, outside of the CARB stamp, is the warranty, hence the higher cost. I'm not happy, but not quite as irritated either.
The only other thing in the Executive Order verbiage, is a reference to that the CARB cat was tested with a certain process, and was shown to NOT throw any false CEL's. That may not say much, if anything, but it's somewhat noteworthy. Based on what I've read, I wouldn't worry about installing your non-CARB cat on your ZJ. Good luck.
http://ssl.arb.ca.gov/PartsSearchTool/ExecutiveOrderPDF.aspx?AEON=D-182-60