It's not at all a matter of "right" or "wrong." It's simply personal preference. The volume of the drive channel is set exactly where Jeff Bober thought it sounded best. If you run the clean channel clean and use a decent amount of drive, the channels balance perfectly in stock form. The only balance issues come when you crank up the clean channel and use a lower gain setting. This makes the clean channel slightly louder than the gain channel. The resistor mod remedies this but sets the amp up to balance with the clean channel cranked up (so it would be out of balance with the clean channel running clean).
FWIW, I did the pot channel balance mod to my Buddas because I like the versatility. It does change the response of the drive channel a bit, but for me, the versatility is worth it. For some folks this is not the case.