TypeScript uses npm as a package manager yes, but there is unfortunately no support for using Node within TypeScript yet on Visual Studio. There are definitions for node/express/etc, just cannot compile them directly in Visual Studio and also have debugging (unless the linked package in the OP has changed that).
Looks correct to me and makes the most sense to build the tools in the language TypeScript compiles to. On another note, it would appear they will be adding TypeScript support in the beta[1], which makes me very happy.