They're not talking about the interface. They're talking about the underlying nuts-and-bolts stuff.
No, they're really more talking about the interface. The underlying nuts and bolts are already pretty much the same, in that Windows, Windows RT, and Windows Phone all share the same NT kernel. But above that there is plenty that's different from platform to platform. What Nadella wants to do is unify the development model and allow developers to create apps with UIs that react and readjust depending on the screen size of the device they're running on, much like how modern websites can support multiple screen sizes. All this talk about "one version of Windows" stems from a single, oversimplified comment Nadella made on the earnings call. When asked about it later, he completely backtracked and said there would not be any such thing.