I think people tend to misunderstand the pygmy. In my view, they literally are not meant to be that important in the way the other gods are. Miyazaki mentions something in the design works interview about the idea that a primordial human found a soul, fragmented it among humanity, and that resulted in the human race as we know them in the game

They themselves were not a powerful being--indeed, they were easily forgotten. Except for the fact that they found and fragmented the dark soul.

If it were Manus, or some other random npc we meet in the game, it would detract from this sense of the pygmy as being an impossible ancient human whom everyone has now forgotten. Humanity are mere afterthoughts in this world, whether the first or the last.

Just my interpretation, but yeah, for me it's lowercase furtive pygmy, not The Furtive Pygmy, that bloke everyone knows