I'd like it if someone could post a recording from a real NES of track 4 of this Mach Rider NSF, or from in the main game.
http://www.angelfire.com/nc/ugetab/MachRider.7z
I guess that means part of what I was hearing in FCEUXDSP was an error, and that the double tone was actually more correct. With that audibly confirmed by the hardware, I think it's quite nearly time for me to get back to fixing 4017 errors.
Also, thanks for taking the time to do that for me. I hope now I can be a bit more confident about the end results of my NSF hacking.