Alfred triggers app-specific shortcut

Describe the bug
I have a Chrome specific shortcut - double press "Arrow Down" to emulate "Command + Arrow Down".
When I have Chrome open and I invoke Alfred on top of it and type a few characters and start scrolling down in the drop down menu in Alfred app by pressing "Arrow Down" key, if I press it fast enough it will trigger "Command + Arrow Down" inside of Alfred.
I have added Alfred to exceptions in BTT configuration to completely disable BTT in Alfred but it still triggers the shortcut.
I guess it has something to do with the way the Alfred prompt is invoked without stealing the focus from the "underlying" app but I'm still wondering if it is possible to fix this problem.

Affected input device (e.g. MacBook Trackpad, Magic Mouse/Trackpad, Touch Bar, etc.):
Macbook keyboard

Device information:

  • Type of Mac: MacBook Pro (Retina, 13-inch, Late 2013)
  • macOS version: 10.13.6 (17G65)
  • BetterTouchTool version: 2.530

Unfortunately in case of Alfred (or Spotlight) the active app remains the same, so BTT can not know whether Alfred is active as the system doesn't tell BTT the active app has changed. Maybe Alfred has some mechanism to let other apps know, but so far I don't know of any.

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this is unfortunate because I really was enjoying setting up single key shortcuts - for instance "r" to reply to Mac Mail instead of "shift-CMD-R" - and it works great (conditional focus role is assigned) but it all fall apart when I have an email selected and I try to use Alfred and type "r" anywhere in the Alfred search bar. So there's no way to read that the Alfred quick search window is open? Would love to filter (exclude) that into conditional parameters.

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Having the same issue with Spotlight and Push Notification Replies. Has anyone found a workaround?