Yeah, but also remember that the VRC6 was only ever used in a few games, all Japan-only. Same goes for all the other sound expansion chips. The American NES (as well as PAL regions) don't have the circuitry to support enhanced sound from expansion chips (at least not without modding the console), so it's not really fair to expect NESmaker to support them. That's also the reason why we never got NES games with enhanced sound in America and Europe.
Also, NESmaker uses Mapper#30 cartriges from InfiniteNESLives, which isn't the same mapper as the Konomi VRC6.