I know this is an old thread, but I've added a simple "Preprend CTRL to background apps" option to ClonedKeys that makes focusless, targetless, leaderless 2-boxing possible on a single Mac. (Only 2-boxing, not 3+)

Does anyone know the developer? I hope he'll incorporate it into his code base, as I have little interest in forking the project or being responsible for it.