This (counterintuitively)
I wouldnt say that... it does make sense. These are inverse pendulum's after all, so when you think about say a clocks pendulum, the weight is at the bottom. Since these are inverse the weight should be at the top. The motors weight is effectively null as its on the axis of rotation about the axle's.
Not debating anything you said obviously, but it does make sense.
Very good writeup - keep it up 
I have had all the bits of make one of these for about a year now, but I just havent gotten around to starting - too many other projects on the go sadly.
Good stuff
James