Well, I can not agree that it is a part of the design.
It is more like a bug that not has been fixed.
I'm dealing with usability in different applications daily, so I must say that I don't like it.
When You get the menu option close window Ctrl-F4, it should close the window, not just minimize it.

But, I rather put an priority to get the software to work than getting confused over this minor problem.

I'm confused because I'm getting Access violation errors time after time. And have to restart the computer all the time.
But that is an other issue.

- Harald