The issue with using <iframe/> elements is you can't move controls from one <iframe/> to another. Take a look at our Right-To-Left demo of the RadDock control, RadDock RTL demo
; note that you can't move a dock outside of the <iframe/>.
The only approach I can think of at the moment is using different UserControl for each application. Depending on which applications the customers have, you load the respective controls. However this might increase the coupling among the applications, so I am not sure if this is the right approach for you?
I will ask some our senior developers for further information, and will let you know their opinion.
All the best,
the Telerik team