One issue I could see with implementing NMC on top of BTC is future scalability. Specifically, when BTC blockchain gets huge, it would mean that the datacenters that store bitcoin blockchain information would have to also double as DNS providers. I think a NMC blockchain would be much much smaller in size compared to bitcoin, since transactions on namecoin are much less frequest, even if they may hold more data. So keeping the two separate would allow for many more smaller, independent DNS providers, instead of limiting it to just the few bitcoin providers we'll likely end up with in the future.