Hm... Since you asked I goggled and I found some interresting sites which documented the VRC6. I couldn't make out what exactly is the limit for Roms with that mapper. I believe one description told about a size of 256KB, but I do not think that is the maximum size. Castlevania 3 had 512KB with the VRC6 and I think that we could go above 1MB easily. Even Megaman Odyssey and Rockman 4 MI could reach 1MB with the MMC5.
Still, what interrests us is the data responsible for the two additional sound channels.
What to do is to make contact with the guys who made the emulators, like the FCEUX. They could answer all our questions and even help us to make the 163 mapper better overall. All what we really need is knowledge about those things. I will ask Kujakiller first for more information, since he is my partner.
You forget that the mapper always evolved. You could even consider the mapper which came after the first one, that all other games with different mapper were no longer NES games in essence. The chips, which contains the mapper, in the cartriges were responsible that the game worked on the NES. Depending on the hardware in the NES era, we gained more memory for the games from the beginning to the end.
After years the SNES came, because the hardware evolved. With the SNES we were no longer restricted to 24 colours, but up to 256 colours with more detailed sprites.
I am going offtopic, but you must know that with 2MB and maybe even 1MB we might have gone above what was once thought to be impossible for the NES. However memory is not the problem for the NES, but things like SNES graphics are right impossible.
Point is that the reason we work on NES games and not on N64 and above is, because we love the NES with its limitations. Nostalgia is also a reason. As long it keeps the NES flair with said limitations it is a NES game.