Late to reply, we run 2 teeth captain advanced. We had ridden in phase, for a while, then took the time to use the monitors and computer to give meaning to how things felt. During a ride, we stopped and tested various settings after a baseline of in phase. For us, at the time, after several setting changes, we decided on the 2 teeth advanced. This gave the smoothest spin, easiest to spin 100 rpm constantly and lowest heart rates.
On the off-road tandem we ride in phase. Pedal strikes are a large concern and spinning off-road at 100 revs is a bit to bouncy for the suspension and tires.
The best answer, it just depends what you like and what works well for you.