I think if you have the time and the inclination to do this, it would be an amazing project! As I alluded to earlier, my DIY experience consists of simple analog circuits, so I don't know anything about how to work with digital electronics. I do have about 25 years of experience working with FM synthesis of various types, if that's any help.
Have a look at this if you haven't already- there is some decent documentation for the YM2608 here, which is an earlier implementation of the YM2612 that required a separate DAC chip.
It also has some other extra features, but the FM synthesis and SSG seem to be the same from what I've read.
You're right, you could totally buy some cheap Alpha pots in bulk and save a ton of money. I know quite a few people who do that.
The big question is, how many functions of the chip are you trying to give direct parameter access to? Some things could maybe live in some sort of menu rather than being functions with a hands-on encoder.
Yamaha's usual way of keeping costs down was to have each function on a selection button with one or two data entry sliders and inc/dec buttons to change values.
YM2612 is a 4-operator synth, with 8 possible algorithms, very much like the Yamaha DX100 or FB-01. Unlike those, it has stereo output, plus there's the SSG sound generator (3 pulses and a noise iirc).
So at the very least, you would have to duplicate the individual parameters four times, one for each FM operator, and that's just for the usual stuff like coarse and fine frequency control, output level, envelope controls (I don't know how complex the envelopes are on YM2612, but Yamaha runs the gamut from simple attack/decay EGs to an 8 parameter setup with four env stages (level and rate control for each)).
It's so much to think about, it breaks my brain!
Because that's assuming you are just going to make Megadrive sounds in real time and play them from a MIDI keyboard.
If you actually wanted to make it function like a Megadrive, you'd have to make it multitimbral so you could have a different FM patch on each MIDI channel, up to how ever many voices the 2612 supports.
Just thinking out loud!