That's a WIndow's and Dolby working together problem.
Does whatever video card your outputting through HDMI support Dolby Atmos?
I'm not sure where you would go on a PC but if you're LPCM sending signal to your AVR, maybe just try Bitstream for that one game.
As for headphone use, I think the DTS:X sounds better with headphones, as they have individual headphone profiles.
I'm not sure if anything can help your Bose headphones
. But yes, what you describe is how to make it work, you can trial the license and trial the DTS:X one, see which one sounds better to you.