Actually, now that I've looked at yours a second time. I think the latches need adjusting to bring the lid down more and then your adjustable bumpers need to be moved outward to get the edges of the painted lids more in line with your metal bodywork. Make sense?
And this is where the art of bodywork comes in. That's not a simple two step process since adjusting the bumpers will impact the vertical height of the doors too. Could take a few iterations of both to get them mostly lined up. I say mostly as these are not designed to be made perfect, even with a lot of adjusting.
Also, making the lids tighter means they will be harder to close since you now have to compress more of the gasket around the opening. I have seen a few RamBox lids so loose from the factory that they didn't even touch the gasket, i.e. they were not waterproof.
I still prefer to do these sorts of things myself, and I'm no body guy by any means. It's just that even under warranty, there's no risk of an hourly tech messing something else up, forgetting a bolt, etc. and I can get everything tweaked well short of the time it would take to drive to the dealer and back. The only time I'd have the dealer look at these is if Ram came out with an updated part that could be replaced or I had it in for other multi-day work.