I had a VERY similar issue, but with an even further problem. I have DVI-D going to a 144 HZ 1080p display (that can ONLY go past 60hz in DVI-D mode, HDMI will not output 144hz on this particular unit), and HDMI audio going to an HD Audio Yamaha unit that does DTS-HDMA, Dolby TrueHD, and LPCM. As you all surely know, only HDMI can carry those sound signals so I have to use that and cant use opti, or coax, or anything of the sort.
My issue was not the fact Nvidia's card was detecting the Yamaha unit as another monitor, that didn't inherently "bother" me. My problem was that the only way I could keep my 144 Hz refresh rate was to "extend" the display, as duplicating it cut the refresh rate down to the HDMI's max capability. Disabling the display cut my HMDI audio,and leaving the display extended, meant annoyingly being able to drag things off screen.
So what to do?
I Went into the Nvidia Control Panel and manually cut the "Yamaha's resolution (lol)" down to 480p, with a 30hz refresh rate. This made it technically "impossible" to span the displays, while still leaving the span setting on and gave me back my ability to not throw windows into the abyss past the right bordfer of my screen, whist still keeping my 144 hz refresh rate.