It comes from Germany because it's dead center and that's where Amazon's monster EU warehouse is. I had one come from Italy, I think (that must have been due to out of stock).
It makes sense if you think that they move palettes or even whole trucks, not individual parcels, so it's easier to move a palette from Germany to Netherlands and distribute it, than move individual parcels in Netherlands. It doesn't always make sense, but shipping rates and regulations rarely make sense anyway.
Kinda off-topic but not really, the same way you can't bring your own 0,5L bottle of water in the airport, but if you buy it from them and pay for it AFTER the check-in (and give them your sweet money), you can bring a 0,5L bottle of water in the plane. Or spirits, cosmetics etc. Someone, somewhere, decided it makes sense.