*I am not an expert by any means. If you have a different opinion, please share it!*
To me, what I think it boils down to, is that the audio in the GG (and master system by extension) is just not..... that.... interesting. 3 square waves, one noise channel. So my question is, the Gameboy can do all of that, and more thanks to the wav channel. It can be programmed as a square wave channel if you want, but does anyone actually do that? Probably not much, because 3 square waves is just not that interesting.
It's not like the chip community hasn't ever dug up an ancient console though (see houston tracker). But there's still some element of uniqueness that drives a lot of that.
Add on top of that the relative obscureness of 8 bit sega consoles, and I think you get to where we are today. When was the last time you saw a master system in the wild? I don't think I ever have. Game Gears are a little more common, but not a ton. I mean, there is exactly one GG flash cart out there.
That being said, I like the idea. I'd love to hear if anyone else has any other opinions!
EDIT: Even further, the SN76489 is still readily (and cheaply) available. As much as I hate to say it, if you really wanted a GG tracker, you might be better off just building a whole new tracker interface based around an arduino or something. Like for real, the whole think could be made for under $50. cram it all in a gameboy pocket shell or something.