The EITMS is set up differently on the Twin Cooled bikes, so that it's triggered strictly by ambient air temperature and not cylinder head temperature. I assume that change was made because they expect the water cooling to keep the head temps controlled in a much narrower range and the system wouldn't kick in as often. Don't forget that Harley has always claimed EITMS is all about rider comfort, and shutting down the rear cylinder does pump air through the head and exhaust which will reduce the heat felt by the rider. I would suggest if the rear cylinder shutdown bothers you, and if you don't have an issue with the heat coming off the rear cylinder and exhaust when stopped, then you should disable EITMS altogether. It's a simple and easily reversible process, so go to the owners manual and follow the directions to turn it off. If you like it that way, fine. If you don't, then just repeat the steps and turn it back on.
Jerry