If it were up to S&S, I would guess that they program a bit more fuel to the rear cylinder, right side. That would keep it cooler as less air gets to it in a motorcycle.
Actually in cars, the driver's seat is ground zero for right and left. I know in the UK it may be near side or far side. Not sure which is which though in that scenario. So for use US guys and the European guys, sitting in the driver's seat, left is left and right is right. The S&S would be front cylinder left side and rear cylinder right side. It can get confusing when you refer to LOOKING at the car from the front for left and right.
Not sure if timing can be adjusted for less advance between the cylinders or not, but I'm sure fuel can be adjusted, at least on Harleys they are. Theoretically, there should be no difference in cooling capacity between left or right cylinders in a M3W. Oil cooling is routed the same for each head, so that is probably not a cause. Not that it would help, or that it's really a problem, you might try one heat range cooler spark plug in that head and see if the temp equalizes. But ever if that did help, that's only a band aid, not a cure.
The problem with all the information we get from bikes and cars today, knowing can be a problem. In the old days no one complained of Harley's engine oil running hot. But when they put oil temp gauges on the bikes, everyone was complaining about how hot their bike was all of a sudden. I realize that on the M3W the exhaust pipe was the determining factor to lead one to investigate cylinder head temps. Other than the different color on the header pipe, sometimes you're better off with your head in the sand...

Out of sight, out of mind. Back in the mid-60's and through the 70's, we had a marina in Michigan and sold snowmobiles in the winter. Early on there were no speedometers on any snowmobiles. Everyone had their seat of the pants dyno saying they were running 70 and 80 mph. THEN a couple years later snowmobiles had factory speedos. Lots of people retrofitted their older snowmobiles with new speedos. Guess what, their snowmobiles all of a sudden weren't running as well as they had before. Like I said, some times ignorance is bliss...

Trust me guys, I'm not saying that you shouldn't find the cause of the extra heat, but other than the header coloring, it's probably not doing any damage.
I'll get off the soap box now!
Have a great week guys!!!