I didn't read the whole topic, because it's so big, but only the last message. So I'm sorry from advance, if, by the chance, I missed something important or repeat something already said.
But I think that your problem is, that you take the value of ink, bought at the worst offer (i.e. in amount of 1600), as the base value. I.e. that you think that the base value of 1 ink is 1.99/1600 = 0,00124375 $, since you buy 1600 ink for 1.99$.
But for me it looks that "the base value of ink" is the value, which we get from the best offer: 40000 + 20000 for 49.99$. I.e., I'd say, that the base value of 1 ink is 49.99/60000 =~ 0.00083167$. In this case, the "base" value of 1600 Ink would really be very close to 1.33$, as it seems for you as for creator.
So I think, that the "hidden fee" arise from the "fine", which we have when we buy small amount of ink.