The current color picker that comes up when editing a color scheme is only able to pick colors from within its own window and not any other area in the desktop.
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Either I'm not understanding your request properly, or the color picker does work as you're requesting. See the following YouTube link - video is too large to upload directly to Phab.
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I could be doing something wrong and I ran into a bug in my system, but I am unable to select anywhere outside the color picker window. I will update and report what happens.