Exactly, and this highlights the big difference between using headphones and using speakers. When you listen to some stereophonic music with one of the instruments panned completely to one side, through speakers that sound will only play from that side, however the sound will bounce around your room and you'll hear it in both ears, and the difference will tell you where it's coming from. But when you listen through headphones, you don't get this effect, and it sounds weird. With modern computing devices, it shouldn't be that hard to run the music through a filter that mixes the two channels when using headphones to avoid this problem. I wouldn't want to mix them to mono (that sounds bad too), but just a slight reduction of the stereo separation would be good.
I wouldn't know because I consider all those effect libraries, mixers and presets ("Concert Hall" - who would ever want that?) that usually come with the audio chipset driver suite as bloatware and try to get rid of them, or at least never touch them - but it would surprise me if there weren't anything that affects the amount of stereo separation...?