i broke my engine in with the basic oil it comes with like you supposed to to help everything seat then changed out the oil for 300V at the first oil change because i was so pleased with it from my previous bike. the 300V is always clean and keeps its same basic colour for my engine. the 300V is supposed to have the best rating you can for how well it lubricates gears and other parts to keep them from contacting metal to metal its supposed to retain the film even under high pressure. i believe thats part of why it stays clean the engine isn't wearing out and dirtying the oil.
i just pulled the engine on my '15 R1M and tore it down to do my motor build and the inside of the engine is SPOTLESS. no black, no dirt, no wear marks on any of the transmission gears nothing on the shift forks the engine looks like it has maybe a couple hundred miles on it. some slight marks on the main journal bearings but i believe thats from the initial cold starts in winter to warm it up once a month.
i was told that the 300V doesn't meet yamahas exact spec for what they will warranty for whatever reason, but i know ducati use the 300V in their bikes it was what dealers where i am used as the standard so that leads me to believe its just yamahas criteria isn't met and not that theres an issue with it lasting.
as for the oil getting black from running rich thats more of an issue if your rings aren't seated properly. as zdamans oil analysis showed the fuel in his oil is negligible. its more concerning the oil mist going into the air box and causing carbon in the combustion chamber. he's running his oil more miles then a lot of people are and changing it once a season so thats even longer then the recommended 6 month intervals and its still within spec. thats good to see in hard facts. id say the colour change is the additives just darkening with the heat cycles. all the facts and studies and data sheets are out there on all these oils its probably better to look those up then get hearsay and urban oil legends from a forum.