With the videoconferencing application, it is just that, an application and will function like any other Windows application. When you take PowerPoint to full screen it will come to the foreground of the display it is shared on, thus covering up all other applications. That is the way it works.
A couple of solutions: Use 2 screens and put the RPDesktop on the 2nd display.
Do not go to full screen with PowerPoint, and tile your windows the way you want it.