If I remember correctly, much of.these issues started when Toyota engaged Dana to design (and build?) the truck frames. I've never been a fan of the results.
Dana built the 1995-2004 frames as well as the 2005-2008. The factory was sold or a name change in 2009 so technically frames from 2009 on come from a different supplier. I think they were actually made in Mexico at Metalsa, which used to be a Dana plant.
What I think isn't mentioned is that Toyota is only one manufacturer that uses Dana-made parts. Ford has a lot of stuff made at Dana and they make other components for heavy machinery and stuff. Only Toyota frames have this rust? Maybe it's a specification of the steel, paint or corrosion protection. Dana is going to do what they are contracted to do. If Ford tells them to use a wax coating and Toyota doesn't then is the problem really with Dana?