It would be cool if you could specify the articulation order.  Is there any calibration reason why it does them in specific orders?

If you are off line programming you could specify a probe head that can't do a negative A rotation.  Just have to switch it back when you are at the CMM.

Probably the real issue/ fix is that if you are using CAD the software "ought" to be smart enough to know that it is going to pass thru the part and either warn you or not pick the negative.   On at least the later versions it does ask if the proposed angle change is OK.