This whole conversation is built on a hypothetical model that uses water, that's why he talks about water:
Newton imagined the existence of two tunnels, one from the North Pole to the centre of the earth, and the other from the equator to the centre. If these tunnels were joined at the centre, and filled with water, then as the earth began to spin, water would start to flow from the pole towards the equator.
If he had made the model use mercury instead would you think that the ocean is actually made of mercury? It's a hypothetical model under discussion.
He makes it clear that if the rock portion of the earth were to form higher or lower than the threshold, you might have a high-and-dry equator or a miles-deep-ocean equator.
...if the rock had not distorted to bulge by the appropriate amount, then the whole equator would be flooded; whilst if the rock had somehow frozen in an over-distorted shape then the whole equator would be a mountain range.
I read this article and it is clear that he's talking about the overall shape of the earth, and not whether the bulge is made of rock or water.
So if you want to assert that the ocean should be miles deep at the equator on the globe earth model, you need to find the portion of this article or another article that resolves that "If the rock had formed one way" question in the second quote in this post. You are the one making the affirmative claim that centrifugal force should make the ocean miles deep, and this article clearly states that it cannot distinguish between whether the equator should be high-and-dry or deep ocean.