Engine heights are like lower unit lengths. The Long shaft standard gearcase is a 20″ case. Most transoms are in the 23″ range for these engines and the actual engine height is in relationship to the lower hull.
Thus the engine is properly measured in this fashion, as shown above.
The center line measurements are more commonly used as things progressed to the high performance thoughts from fast boat fans. Though this is still the proper way to measure engine heights. Which is why you will always buy a 20″, 30″ or a 25″ gearcase length.
BCB