I've read many reports similar to yours, where the system kicks in at what people believe are ridiculously low temperatures. It has led me to believe that H-D went a little overboard when they set the operating parameters, to try to head off the high heat complaints they knew they were going to get with the larger engines and leaner EPA legal fuel settings. I'm not aware of a way for the dealer to change the temperature setting where the system kicks in, but it may be worth asking the question.
If you want to determine if your's is working as designed, it will require a little detective work. The system responds to the engine temperature signal from the sensor mounted in the left rear of the front cylinder head. The first bit of detective work involves monitoring the head temp while the bike idles until the system kills the rear cylinder, and then comparing the temperature with the specs for the EITMS. It would also be helpful to verify that the sensor in the head is actually accurate. If one has the proper equipment it should be a piece of cake to verify the system is operating properly. Good luck finding a dealership to do this for you, however.
Probably the best advice for those who don't like this system is to turn it off, which the rider can do himself following the instructions in the owner's manual. If you worry about excessive rear cylinder temperatures if you turn it off, get the bike tuned. There are several threads on the site concerning changes to the exhaust system and tuning that help reduce temps.
Jerry