That is certainly inconvenient, especially with the boards that make more extensive use of this feature.
I tried it again myself - I can reproduce it with Arduino IDE 1.8.13 (Mega2560 <-> ATtiny85) but not with the 2.0 beta4 . I will keep you posted if it should happen (again?)!
My concern is this could result in confusing behavior for beginners. The output window provides feedback on what has happened, so if it disappears immediately after the process finishes then a beginner might be left wondering what was the result. It could be enabled via a setting in the “advanced” section though.
I see what you mean - and I agree that it could be an advanced feature. I like to use the full height of the screen for my code, but on the other hand I like to see what’s going on when compiling and flashing. Auto hide (like in VisualStudio, the output window hides to a tab at the bottom, when I click into the main window) would be perfect. The window would remain accessible without blocking many lines.
That would certainly provide a closer emulation of the classic Arduino IDE’s Serial Monitor. Do you have a specific reason for wanting it in a separate window?
The same reason as above, I like to keep my code window clean. With 1.8.13 I move the serial monitor to the second screen, so I can watch outputs while making changes to the code without wasting space.