Maybe im not explaining it well, sounds like youve missed a bit of what im trying to say!
Tried this on 2 Ubuntu machines an a Windows 10 one, identical behaviour.
I see whats going on now, but I still want to turn it off. (and now REALLY want to turn this off!)
If you run a game and have it playing in a floating window (or if you have the game running in a NON floating window), theres 2 sections to that new window, the top bar with the pause/play/input/2d/3d/eye... buttons, and the lower bit that displays the actual game.
Theres a highlight around that lower part, NOT the entire floating window. shown (green highlight!) in my lower image.
When it is highlight you can use the keyboard keys assigned to trigger whatever they do in the game, player movement for example. Keyboard focus is set to work on that game window.
However, if you click on any of the pause/play/input/2d/3d/eye... buttons, or even not on them, resize that window, or move it slightly - just to see a setting or whatever underneath it, which is how this is tripping me up - this focus highlight on that GAME window turns off, and any key presses are now passed to the godot editor BEHIND as keyboard shortcuts if thats the key you pressed, or as the script editor is open, inserting text into the code or removing it.
To get focus back into that lower section of the floating GAME window so you can use key presses in your game again, you either need to click in that playing game section, or hover the cursor over it for second.
The floating game window is ALWAYS on top, though it may as well not be, behaviour has changed as if its not even there! :/
Would a vid clip of what im trying to explain help?
Trying to replicate this again, I again still managed to unknowingly delete selected lines of code with the editor tab open behind 🙁 Im going to put in so many errors and change things in the background without realising.
Figured this out as i have arrow keys for movement, which, if the scipt tab is behind, just moves a line up or down, but 2D / 3D tab open, scrolls through the editor tabs (Scene/Import/Scene1/scene2/Inspector/Group etc...), other keys started triggering other editor shortcuts!