The grease or any silicon grease will work. But, the only lubes the seal. The question should be, what comes loose to allow it to rattle? There is something in the mechanism that is wearing allowing movement.
I actually don't use my roof that much. A few times if that in the winter. So wear and tear idea is not it. My tracks inside are actually super clean after two years of owning the truck. There is also plenty of factory grease all over as well.
This is my take on it. And after using a couple of synthetic lubes and Krytox over the last couple of years, you start to learn.
When the seals have no lube on them and become dirty, I believe the whole panel cannot float on the tracks and stick somewhat to the roof line of the cab. While there isn’t much in torsional forces and flexing of the cab, there probably is some very unmeasurable amount. Along with jolting bumps from the road, this fights the sticking glass panels and moves them, just enough to wiggle on the sliding mechanism. Hence the rattle sound. But the rear panel is fixed, how can that be? It’s still anchored down, but somehow also can be forced to wiggle around, if it’s seals are not clean and do not have sufficient lubrication. I know this to be fact, as I cleaned and lubed only the front panel in the beginning and still had the majority of the creaking and rattling. Once I did the same to the rear panel it was super quiet. As
@JohnyPython said, this is a large heavy panel and apparently if it can free float as it wants, it’s gonna flex and move all it’s anchored too.
I bet a new truck that sat on the lot for 6 months to a year before anyone ever purchased it. Would do the same rattle and creaking, as the seals would be dirty and dry. It’s all about the lube, amazing and as basic as it sounds. Does washing your truck a lot actually help to wash out the lube on the seals? I think maybe so. It it won’t help much to clean those seals. As mentioned in the tsb, a credit card and rag works really well.
Long winded but my take on it.