Personally, I disagree with the "never rest your hand on the shift knob" rule, just like I disagree with the "always keep your hands at 10 and 2" rule, or the "don't put your elbows on the table while you're eating" rule. Those have all seemed completely arbitrary, bordering on superstitious, with no perceivable downsides or consequences for doing it.
I say, put your hands wherever it's most comfortable, and you're probably fine. I've been driving stick for 11 years, and sometimes I rest my hand on the knob, sometimes not. Sometimes I have one hand on the wheel at 12 o'clock, and other times I have both hands at 9 and 3. Do whatever is best for you, I say.