I’m a web developer myself and know the ground and background, but your assumptions -sorry- are wrong.
YouTube and Prezi use the same Flash Player.
The difference is, that it seems to be that the Prezi Online Flash application uses the
StageDisplayState.FULL_SCREEN_INTERACTIVE flag, and the Y ouTube Flash application not. (Remark: the Flash Player runs the Flash application, and the Application is developed by your developers)
So the only one who can answer this is a developer.
I know that 1st Level support should keep away as much as possible from 2nd Level support, and that noone should disturb the developers
But I think this is an inconvenient behaviour which is often discussed and criticised. Maybe noone thought about it, why it is built in that way.
Another workaround could be that there is the ability to switch from the small box in which a prezi shows on prezi.com to a bigger. YouTube offers this as “cinema mode”. Maybe this is enough to watch a prezi without full screen mode.
To watch a prezi now in this really tiny box destroys the beauty of Prezis, and you HAVE to switch to full screen mode. And I dont want to write to all my Prezis: “When you switch to full screen mode, please click on “Accept”, you can trust it. I know this is unusual, but thats how it is”