When the game is manually paused with the pause keyboard shortcut, keyboard shortcuts ignore windows that are still interactable, behaving as they would normally if the windows were not open.
The best example that I have that demonstrates why this should be considered a bug is with the tech tree screen. To reproduce, first open the tech tree, then press the keyboard shortcut to manually pause, then press escape. I would expect the keyboard shortcut to be picked up by the tech tree screen since it's still fully interactable, resulting in the tech tree screen being closed, but instead, the "game menu" window is opened, and it appears underneath the tech tree screen. You can even close it again underneath the tech tree screen by pressing escape again.
The main reason I care about this issue is for using the Factoriopedia while the game is paused - the back/forward buttons work, and they're even able to switch back and forth between the Factoriopedia window and the tech tree screen if your history stack is set up for it (for example, if you click on an "unlocked by" box in the Factoriopedia), but you're not able to use the keyboard shortcuts to do the same thing - only the buttons work.
[2.0.32] Unexpected keyboard shortcut behavior when the game is manually paused
Re: [2.0.32] Unexpected keyboard shortcut behavior when the game is manually paused
The intent is no game GUIs work while the game is paused. Through keyboard or mouse.
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Re: [2.0.32] Unexpected keyboard shortcut behavior when the game is manually paused
I see - it seemed like being able to use the Factoriopedia while the game was paused was an intentional decision. But in that case, I guess the bug would be that the Factoriopedia, tech tree screen, and tips and tricks window are still interactable when the game is paused, and that they all draw over the game menu window instead of under it.