I'm not sure how to log the data while playing a game, but I think you are right about it not forcing you to use one or the other.
In Wii Sport Resort there is an archery game. In it you hold the remote so the sensor is sticking straight up in your left hand. Then you use the nunchuck as if it was the string. Hold z and start pulling the nunchuck back, then release z to fire. I find if you spin the wiimote around the Y axis (or whatever axis it is that goes though the sensor) it rotates the bow in the same way. Since this axis is vertical, this rotation would be perpendicular to gravity, so it must be the MotionPlus that is taking the rotation, yet the nunchuck is being used as well.