I like to have FFXIV open to hang out/talk with friends while I play other games, this generally isn't an issue. The issue arises with Destiny 2 ALWAYS accepting controller inputs even when it is not the main window I'm tabbed to. Even while here typing on the forums, my controller can still operate Destiny 2 while my browser is the focused window.
Video showing the issue.
https://files.catbox.moe/08ez0y.mp4
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This was a steam issue for me when I had it, steam injects it's controller support at the top level so it locks on to any controller activity when it's running. Not super helpful but maybe you can check out the steam controller settings.