While I believe this was true in the past, I don't think it is anymore. Generac is very interested in reducing install time for contractors with the goal of reducing end user price and moving more units.Another example is generac requiring ground rods for stationary generators when they are not SDS. AHJs would have to enforce that. Generac did that as they didn't understand generators and grounding electrode requirements, was easier just to say ground rods required. Mike Holt tried to work with them for a while but gave up
I don't believe that the instructions can give you permission to do something that is not code complaint. They can exceed the code but not the other way around.
I think that the counter point to that is sometimes you may see stuff that you assemble from components that wouldn't be compliant on their own, but are compliant as a listed assembly. And it would be a violation to modify the manufacturer's stuff.