The rim shown in the calculations below is not a GM rim:
It has a much larger ERD and therefore needs longer spokes.
The spoke calculator is not wrong, but it can only give the correct spoke length if you enter the correct ERD value:
For the above calculations I simply entered a guestimated ERD measurement for the 26" Deep "V" GM rim, as I don't have a bare rim to measure accurately, but the value I used is probably within a couple of millimetres of the rims actual ERD.
The Magic Pie III
(Magic Pie 3) is definitely not smaller than a Magic Pie 5.
If you take a look at the picture below you can see that the MPII and MPIII use exactly the same length 110mm spokes for the GM 26" rim as the MP4 and MP5:
Putting the elbows on the outside of the flanges do not present a clearance problem as they are even further away from the chainstay than the side cover of the motor:
Hopefully this post has covered your concerns.
Alan