OP updated with the Launch + Preorde exeption... Amazon high accuracy explained for these cases... I will add the multiple SKUs exceptions late too.
For now nobody found a examaple that didn't fit in these exceptions and disprove my OP theory (close to fact already).
LAUNCH + PREORDERS EXCEPTION
In easy terms NPD shows everything sold, including the preorders in previous months, in the launch month but Amazon shows the preorders in the month that the preorder was made.
So it won't be accurate in the launch month for hardware and software because you need to look the previous months to have the real ideia of how the game/console performaned in the launch month.
Eg.
MW2 (360) > SMBWii in NPD November
SMBWii > MW2 in Amazon November
Now look the places of MW2 (360) preorders in the previous months in Amazon...
August: #37 (preorder for November)
September: #20 (preorder for November)
October: #1 (preorder for November)
November: #4 (sales in November)
Overall the Amazon shows what NPD shows when you check the previous months preorders.
Same happened with PS4 vs Xbone in November NPD... PS4 > Xbone but Amazon November had Xbone > PS4 because PS4 didn't have any unit to be sold in November anymore... all sales are preordered in previous months before November.
