Those windows are not overly functional. If the debugged program does not hit a break-point, there is usually not enough time to read the message. And with plenty of tests being run one after another, those windows can be somewhat disturbing, too. I am fine with changing the default.
I find console output much more usable than the popup window. The popup is either closed too early (before I have a chance to see the message) or I hit a breakpoint and then I don’t see the message (because the window cannot be redrawn or resized when the program is paused). Also, the popup’s content does not appear on dashboards and cannot be copied to the clipboard.
It would be great if we changed the default to use the console by default.