Yes, the NEHGR appears very thorough and certainly suggests we are only looking at three wives absent some other primary source to connect one of the other wives.
It appears to me the two Unknown Unknowns would be the same person as NEHGR has them, not two different wives (which may be read unsourced at Find-a-Grave). It appears he did have two sons (both lived) named John. They are differentiated and the second is referred to (in the will) as the "myddle" which I interpret as the middle of the three sons by the first wife. If the two Johns had different mothers, there would be no explanation (that I can think of) for one being called "myddle."
Star for the NEHGR link -- somehow didn't come on my radar so major thanks for finding it.