That is because Keyboard Maestro cannot do that (unless you click to make that window the frontmost). There are some things that BetterTouchTool can do that Keyboard Maestro cannot which is why it's handy to have both Apps.
I think that's the solution actually. I made something for someone recently to send the window under the mouse to the back and it works fine because the first click only brings the window to the front; no issues with accidentally clicking elements.
BTT is surely a handy tool. I used it for several years, but found it didn't play nicely with my new Wacom. Even on my other computers (without Wacoms), I frequently had issues with laggy typing and CPU usage.
Keyboard Maestro seems much more refined and does 99% of what I need it to, in a more stable and, in my perception, less hacky way. The trade off for being better Mac citizen is some limitations with this kind of low level integration with the OS.
Thank you! This is working really nicely. I have swapped out the Close Window for a Command + W keystroke, since I often want to close only a tab in Safari or Finder. I also added Active to Last Application to the Otherwise block.