Just got a reply from them, and here's what they have to say about the last little detail...
The spoke head orientation (all inside, alternating in and out, or all outside) can be used to optimize the dishing of the wheel in some scenarios where the motor flanges aren't centered, and also to help improve the seating of the spoke head. if the flange is relatively wide (head on the outside) or too thin (all heads on the inside). The rear Crystalyte motors have an offset flange that counters the axle offset (which sticks out much further on the freewheel side) so that overall it is relatively centered, and the easiest way to build it is with all the spoke heads on the outside as in the 1st pic posted here.