I think that this is an important feature.  Additionally, I've noticed that TO and applications tend to crash if moved around in TO.

I suggest that TO treat apps as follows:

Apps are a special form of window.

Apps have their own color (I'm thinking a red tone).

Apps can not directly contain child tabs.

If a user drops a tab on an app then TO spawns a new child window to contain it.

If an app opens a tab then TO spawns a new child window to contain it.

Otherwise, Apps can do whatever Windows can do.  You can name them, nest them with other objects, close them and open them, etc.  

Further, I think that TO should either not appear in TO, or should be treated as an application.