Well, I know almost nothing about Deflemask since I never used it, but from what I know, it's only a tracker, so the Green Hill Zone song you're referring to is likely to be a handmade recreation and not the original thing. But I might be wrong.
Now, to look at your question from a different angle.
As you might have noticed, the VGM format supports a whole lot of gaming system. However, you won't find Genesis VGM files here, as they're already on
Project 2612. From there, you can download the VGM packs for all the Sonic games. Once you have them, you can find some VGM players
right here. And this is where things become trickier, since you can perform channel-by-channel muting in vgmplay.exe and in the Winamp plugin (I recommend to use this, since it can do it on the fly while the former uses an ini), but there is no way to perform instrument-by-instrument muting. There are several cases in which a channel uses the same instrument throughout all the song, but there are other complex songs in which instruments are changed, so I'm not sure if that would be enough for what you're looking for. Furthermore, the same instrument might be used on more than one channel, and recording chords with this system would add another layer of difficulty. The only easy thing in all this is that 2 or 3 channels can only be square waves and it would be trivial to take them apart.
Unless someone can suggest you an easier solution, I'd personally alter the sound data in the ROM itself if I had to be sure to do a perfect job. I'd zero all the parameters of all the instruments except for one, repeating the process for each and every instrument. Then again, I know SMPS and I have a lot of time to waste.