You will be presented with the screen between WM or Android to selecting the OS:
The tool is solely created for HTC HD2. Having Windows Mobile to controls your device applications is awesome, but with Android along will be more productive IMO. And one thing about the tool is, after 30 seconds you have not made any choice it will choose the OS for you automatically based on the last used OS.
Interested? You can find more about AndroidWindowsBoot tool via XDA-Forum.