In 12 years I have fitted several Powerdynamo systems as they used to be called though they were always made by Vape. Both the older type with the external sensor and the new type where the sensor is internal. I have always fitted mine with the black ign coil at the top as shown in the instructions.
Indeed I have just fitted a 2nd hand external sensor type where as delivered the black coil was at the bottom. I found it easy to turn it to the top position but you need to make sure none of the wires get trapped in the process. The unit is working fine even though there is no provision for timing adjustment. You do need to follow the instructions regarding which pair of fixing holes to use in the back plate.
Some, possibly all the Vape units are designed to be used on twins of the Jawa/CZ type which require 2 sparks at 180 degrees per revolution and the rotors even when supplied as part of an MZ kit often had two pickups. I guess that gives a wasted spark. I don’t know whether the black coil needs to be in a different position if fitted to other makes. But for MZs mine have always worked with the black coil and the external sensor at the top.
Hope that helps.