It could be that the passenger side battery sees slightly higher voltages due to location closer to the alternator or something similar; but my guess would be that this is not a significant factor. Again, this is a guess, but I would bet that being closer to the exhaust and turbo, the right side is simply hotter, especially during the summer. Heat kills.
Is it worth rotating? Your call, and depends on how much you enjoy tinkering under the hood. To me, a strong battery is so important to reliable diesel starting that I'd say just replace both of the SOB's before the first one fails. And before I began rotating, I'd probably address the "probable cause" by fabricating a heat shield and/or ducting some cool air. Or it might be as simple as installing an exhaust header blanket. Or a blanket + a heat shield closer to the battery. Of course, then you'd have to decide if you believe those who feel that the exhaust blankets make it more likely to loosen header bolts or crack the header. I don't think that's a real problem, but that's JMO, not a proven fact, and it's based on my "near stock" configuration, not a heavily BOMB'd engine.
I do believe in replacing both batteries at once.