I am by no means saying what your saying is wrong, I totally agree with you.
Based on what the service manual says, the offset is measured at four points around the wheel for an average. The brake side (two grooves around surface) of the hub is the flat sureface where the measurement is taken and the reference on the hoob differes between hoop styles. The pic below shows the rim style I referenced for the slim rims. Measurement "A" is the offset, I believe the offset for the dyna is around 1.1"-1.2" for both the rear and front. My rough measurement for the front slim wheel is just at 1.25" and the rear was closer to 1.5". Believe you me, everything will be as close to center on the frame as possible when I am done.