Yes, it is based on the desired layout. Different measurements will create different PAP-pin-MB angles. Since you need a third measurement beyond pin-to-PAP and MB-to-PAP (or PAP-pin-MB angle) to nail down a layout, they're using pin-to-VAL, which Storm and Morich also use. You could also use pin height above the midline.
That system seems confusing to me because, like you, I'm used to pin-to-PAP/MB-to-PAP and pin-to-PAP/PAP-pin-MB angles, but it will do the same job. I would not know how to relate pin-to-VAL and MB-to-VAL to the usual 4x4-type layouts and angle-based layouts without more experience.
It's just another layout system, in the end they're all simply theoretical models that sort of fit experimental data for various pin/MB locations. The 4x4-system might fit the data better in one place than another, the angle based system might fit it a little differently. You're trying to predict what the ball will do using those models and they all have their strengths and weaknesses while trying to account for the zillion extra variables that you have very little control over (speed, rev rate, rotation, tilt, the oil pattern as it's laid down, the lane topography,...).