Per @DanBeale's suggestion: The way I have seen a presenter switch to an application away from PowerPoint without being displayed on the presentation video output is to do it on a separate screen when you extend your desktop via a projector. This is the same behavior you see on a MacBook when you extend your desktop via an external monitor.
In other words, I do not think that what you are looking for is a PowerPoint feature per se. This behavior should be similar in Windows as well.
For example: Whenever I attach my MacBook to an external video source, say a Vizio television, I typically end up using Apple's mini-DVI to VGA adapter. Using the MacBook's video output port brings up additional options in the Display settings in System Preferences. If I choose to extend my desktop rather than mirror it, then I can use the Vizio television to display anything I want (PowerPoint, Keynote, Hulu over Safari, etc). As I do this, the MacBook's own screen remains free for me to use any way I see fit. This screen is not shown via the television.
You can achieve the same results using a projector rather than a television. Hope this helps.