So I set up the Window Location rule to prevent deactivation of the window I'm gaming on.

(Never mind that I had to make my large monitor my Primary display to make it all work even though I wanted to keep my smaller one as primary)

The preventing of deactivation works like a charm, problem: it maintains keyboard focus even as I'm using other applications.
If I stop to type on a messenger, every keystroke is being sent to the game. (Which in most cases in not good)

Is there any work-around? Cause this was the reason I bought DF in the first place.

Sending an email right now. It's a shame but it seems attempting to avoid using Steam Big Picture and sticking to just DF has created more problems than it fixed.
Even with the Window Location rules it still doesn't bring everything into functioning how I need it to. (Ex, taskbar tooltip popups only show up in the primary display and can't be moved)

I will likely be reverting my system's display settings to how they were before. I might keep DF around for a few scattered features here and there, but the ones I know that work well for me happen to be available in the free version.
So I'll talk to support and we'll see what we can figure out.