Opening a command palette or another similar popup (including the file recovery interface, settings, etc) in one window blocks a different popup interface from being opened in a second window, even what the second window is selected. It also blocks the ctrl-f search within file interface from being opened in the second window, go to next tab, and some kinds of keyboard movement. Note this isn’t sensitive to which window is the main window.
I originally submitted this as a bug report and was told it should be posted as a feature request. More or less, if I’m requesting it as a feature, then I would like for multiple windows to be independent with respect to open popups.
This originally came up using file recovery. I usually use file recovery in a second window so that I can compare it to the current version of the file in live edit mode, in part just because the file recovery popup interface visibly covers the file in the open tab behind it. I tried to search within the file open in a separate window from the popup and it didn’t work.