How can I make full-screen desktop applications only cover the snapped desktop?

If all you require is to watch youtube videos, you can follow this recipe:

1. Enter this URI in your browser and remove as much as possible of the unimportant contents of the window (address bar, bookmarks, etc.): data:text/html;,<iframe class="youtube-player" type="text/html" width="800" height="600" src="http://www.youtube.com/embed/dfiR1Rde7dI" frameborder="0"> </iframe>
2. Adjust the width and height attributes to perfect the screen size.
3. Change the youtube video ID at the end of the src, after /embed/.
4. Enjoy

This coresponds to the application's viewstate and they way the browser handles plugins. I would call this is a bug in the software because it doesn't change a parameter called the viewstate as outlined here.

The browser should query Windows for the current viewstate and make the necissary adjustments.

The important implication is that the problem cannot be fixed without source level changes to the programs.