Hi BSA,
Honestly I answered from my office and did not check on the bike, so it was a typical engineer answer 
, purely theoretical and not validated by the practice 
So, I totally agree with your explanation. Anyway, it would have been more logical to have the rear axle fixed on the lower tube, but there is probably a good reason for this.
But I guess that this misalignment could eventually take place in unfolded position when putting some effort on the pedal, causing some problems such as belt twisting??
By the way the recommendation of adjusting the belt tension when unfolded is missing in the manual 
.