Hamilton is easily the fastest driver over a lap, as you say he sets up for a race, not qualifying. He both at Brazil and the race before could take half a second out of Rosberg whenever he wanted. When he passed Rosberg in Austin and Rosberg tried to get back at him, he was cruising, Rosberg went half a second faster, Hamilton went 7/10th's faster and re-established the gap, he did this over and over again all season. When Hamilton is behind Rosberg he's under a second and looking exceptionally close to overtaking. When Rosberg is behind it's 1-2 seconds behind, any time getting close to 1 second Hamilton will just ease it back out to two.
Setting up the car to be faster in qualifying and noticeably slower in a race doesn't make Rosberg faster, it gives him an advantage in qualifying one that considering the advantage he could only use to beat Hamilton half the time this season.
If you exclude the two times Hamilton couldn't make Q3 because of technical issues it's almost even when Hamilton has a quite clearly slower qualifying car.