The channels are supposed to be completely separate. Yaw is designed to not affect thrust. For yaw, the reason that one motor spins faster and the other spins slower is that that results in the thrust channel (total thrust) being the same. It sounds like you would want to mix some throttle into your yaw so that if you yaw left or right you get reduced throttle too.
A better solution:
Also be aware that 16.09 has automatic headroom built in it. In older versions it was required that you limit the throttle to 80 or 90 percent to leave a little room for control and stabilization when you had the throttle stick at 100%. Now days the code is smart enough to reduce or increase the throttle when needed. You can run both motors at 100% and when you give some yaw command it will reduce one motor. Edit: For twins, the old code may seem the same as the new code. You can set your throttle curve to run from 0% to 100%. If you need +-5 differential thrust when using full throttle and both motors are at 100% it will reduce one motor to 95. It will try to increase the other motor to 105, but it will clip at 100%. This sort of does what you want, but note that you only get half as much differential as you asked for. The old way was worse for quads though. If the old stabilization had thrust at 95% and needed -5, +5, +10, -10 for stabilization it would ask for 90, 100, 105, 85. The 105 would be clipped at 100 and the quad control/stabilization would not work perfectly. The new way sees that it would clip the 105 down to 100 and so it reduces thrust (all motors) by 5 and so it DOES get the desired -5, +5, +10, -10 stabilization by running the motors at 85, 95, 100, 80.