Just wanted to come here and thank everyone who contributed to this thread. I've been scouring the web trying to figure out why I couldn't make the background of my own, unrelated game project transparent. This thread finally brought all the pieces together and allowed me to do it.
For future readers, assuming you have this extension or are using a DLL extension of your own or something to accomplish a transparent background, make sure you're building for YYC and check "Use legacy DXGI_SWAP_EFFECT_DISCARD" in Game Options > Windows > Graphics.
And also make sure you're running draw_clear_alpha(c_black, 0) somewhere in a Draw Event before anything else is drawn, ideally in the Draw Begin Event of some game controller object.