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I'd love a hotkey that works when the PureRef is not the foreground app.

If that's not possible, then how about being able to double-click the title bar to shrink the window down to zero height, with just the title bar visible until it is double-clicked again. This would be similar to how palettes in Clip Studio Paint shrink down to a title bar when double-clicked, and then expand when double-clicked again.

You can! In the settings, you can set the shortcut for Always on top, and in the same window, you can also check the System global checkbox, which makes the keyboard shortcut respond even when PureRef is not the active application. Hope this helps!