If memory serves, isn't the whole game on the knuckles cart? It doesn't actually use the sonic cart, it just detects its there and changes what game loads. If that's correct (and someone will correct me if I'm wrong), it would just be a game genie code or patching the rom before putting it on a repro. All seems doable Edit: Ignore the above, I did some googling. Sounds like combining the roms should work. Just concatenate them together and may work. Rom of both together are on rom sites. So just a case of burning to a chip and soldering into a donor (or make a new pcb).
Combined roms already exist so its really more a matter of slapping a bigger ROM in the cart to hold it.
