This is a phrase coined by the author. Although the author outlines the definitions, they don't really make much sense to sense to me.
According to the author's logic, asking yes/no question is "thinking in twos', while asking broader questions is "thinking in threes".
The author alternately refer to them as binary and triadic questions, but again, that seems like strange terminology to me.
In a nutshell, he's talking about asking deeper questions.