I would first check the difference with a mechanical pitch gauge. I found my RC Logger to get a little off when going from positive to negative pitch without re zeroing in the center. Even then, it is slowly becoming less and less accurate, and yes I have re-calibrated it several times.
But as for getting the travels the same. VBar actually expects you to use pitch servo travel to get the same negative number. This is the same as when in the BeastX you have to adjust the positive throw and the negative throw. BeastX lets you do it with software, VBar wants you to use pitch travel. Even the MSH Brain has you use Pitch travel to even them out.
Lowering the swash might help, but if the real issue is the controller not knowing how far to move the servo without the TX aiding, then lowering the swash might not help.