KidSnide
Adventurer
A big paragraph or two front and center of the DMG and PHB that says the DM can exclude anything he/she wants and add in anything she/he wants - whether from previous versions, magazines, the web, or stuff he just made up.
Of course followed by the 'DM consult your players' paragraph and social contract discussion.
Then present the 'rules' as guidelines.
I agree that it would be nice if the books included a couple paragraphs saying how D&DN is a toolbox, DMs and players should work together to decide what type of game they want to play and that you are never doing something wrong if you have fun. That's all good.
That said, I think it's a mistake to treat all the rules the same in this regard. A group could replace their d20s with 3d6 or decide to go classless, and -- if they are having fun and feel like they are still playing D&D -- more power to them. That's a legitimate use of the game, and who are we to judge?
But that's not the same thing as adjusting the obvious dials like, which races and classes are in the world, whether players need DM approval to make custom backgrounds and themes, and whether the game is using gritty or cinematic wound and healing rules. For that type of rule, I think WotC would be correct to provide a "default" version of the rules that they think is most friendly to new characters. However, at the same time, it would be helpful to note in the PH which rules are obvious dials so newer DMs know which parts of the game they can customize and newer players know when they should check with the DM.
-KS