We and OP use the term "Winnower" to refer both to the narrator of Unveiling and to the character in the allegorical Garden. It's natural because the narrator calls itself the Winnower, but perhaps index is drawing a distinction between the two?

I don't think there is a distinction being made on their end at all. Their names and definitions seem to be as follows:

Winnower is just a name given to the Darkness in Unveiling which is mostly, if not entirely metaphorical. The Darkness (Winnower) is strictly a neutral force. Therefore, there's no way the Entity could be the Winnower because by OP's admission, "... there's a reasonable distinction between the sentient math that is the Gardener and Winnower and the beings that they are in the universe."

Problem is, who the hell is narrating the lore book if not a living being? Who is telling us it's coming to hear our answer? lol