I've actually managed using my VoiceBot profile for multiple programs which were running simultaneously with different focus.
Settings -> Configuration -> Profile Marco Actions -> Only run macros on associated application (standard) was also checked, so no issues there.
I did the following at the "Associate this profile with a specific program:", just entered 2 different .exes as per "game.exe|tool.exe". First of all, the tool, which is not fullscreen and will be behind the game rendering window, should be pinned to your task bar (same for the game, for switching back).
By saying "activate slow mo", the tool should go either by some advanced commands (like outta focus key-combo shortcuts like CTRL+NUM1) or the simple way:
* press Windows+3 for 25ms (focuses the tool)
* aim with mouse at X and Y coord.,
* leftclick once,
* windows+4 to return back to your game
It works just fine for me.