I don't know which approach is better, but you misunderstood my previous post.
What I did was I have changed the motor mixing table so that all values are 0, except for throttle. This way you will ensure that the same pulse is sent to every motor. I have also previously calibrated ranges in my transmitter so that when I push throttle to its maximum it also shows as maximum in QGC. You should do that regardless of ESC calibration.
This way you will ensure that by giving max throttle on your Tx, the 'Max PWM' signal is sent to all your ESCs and AQ won't filter it, regardless of the position of the actual board (that's why we have changed motor mixing).
You can then proceed as described before - power on AQ, arm motors, put throttle at max and only then power up all ESCs. Motors/props should be disconnected at this stage, of course. Once ESCs beep - put throttle stick to its minimum position, they will beep few more times - power down ESCs.
No passthrough channel involved in this operation.
After this procedure I have fine tuned the AQ PWM values in QGC to make sure that motors actually start right away when the least possible amount of throttle is applied.
Don't forget to change motor mixing to their default values!
Again, I'm not sure if this procedure is correct (especially given that there are multiple PWM values in QGC) but it has worked for me.