Let's get our definitions down first.  What I call a context 'window' is where the context 'tools' are when they are normally docked (yes, they may be docked in other places as well).  You may use other names.  I'm talking about the window at the lower right that, by default, contains Output, Diagram, Class, Feature Relation, Dependency, etc.  The fact that the 'window' contains several 'tools' is immaterial.  An X box is expected to close the 'window' not the uppermost 'tool'.  The counter-intuitive behavior that you have constructed leads people to attempt to close the 'window' but in fact it only closes the upper-most 'tool' that is in the 'window'.  Now the user is forced to figure out which tool was accidentally closed and then to restore it.

In some other program (whose name escapes me) there are two X buttons.  One large to close the window and one small to close the tool.

I just conducted some experiments.  I moved Output from the context 'window' to the 'clusters' window (Yes, I know it's just the window that 'clusters' happens to be in).  I see the same odd behavior here too.  OK, now I press the X and Output disappears.  I go to View/Tools/Output and it is back in 'clusters'.  Well that isn't what I wanted.  I close it again and select 'Classes' thinking that View/Tools... will place the tool into the most recently selected window.  Wrong!  OK, I grab Output and move it from 'clusters' to (what I call) the context window.  OK, that did it.  Wait!  The X button on 'clusters' is now gone - I can't close it!  OK, I'll press the big Clusters button at the top of the screen.  But, no!  I'm foiled again.  Pressing any of Clusters, Feature or Search will bring up a window but will not close it.  More counter-intuitive behavior.

You spoke about Firefox closing only one tab.  Fine let's talk about that.  In Firefox, each tab gets it's own X button so it is intuitive that pressing the X button will close the tab.  In EStudio windows that contain tools, there is only one button!  In the editor window, one of the tab's contains an X button and the others do not.  So I press on a blank area of a tab to raise a window.  What happens!  An X suddenly appears, I press it and the window is gone.  More counter-intuitive behavior.

Randy