The front cylinder by the nature of its placement gets some cooling that blocks out the rear cylinder. The front cylinder is just sitting there at idle so I don't think it is experiencing any increased stresses because it is not under a load? The rear jug doesn't get cold in the brief time that the EITMS is active unless you are at a dead stop for a long time I would suspect.
I agree with Kevin that there is absolutely no place to find out how things are being set up in the ECU in terms of what gets controlled and when in Harley's thermal management scheme.