Pedrosa for his whole premier class career has had a couple of absolutely dominant races per year, against peak Rossi, prime Stoner, prime Lorenzo, prime MM or anyone else you care to mention, and it was fairly obvious, to Povol and also to me as it happens, that this was the case at Sepang 2015. Lorenzo actually set the fastest lap of the race but knew he had no chance of beating Dani with every incentive to do so. The only time Rossi was faster than Lorenzo all weekend was by milliseconds in the last lap of qualifying, and if he wanted to win the title Lorenzo was the guy he needed to stay ahead of, not MM as MM actually said. The idea of MM’s pace came from a banzai lap in qualifying, something he not infrequently pulls out, and his bike had been skittish early in races all year hence the 5 previous DNFs. Rossi who imo had tried to intimidate MM into not racing him by his statements in the pre-race press conference about the PI race in which I strongly suspect MM actually did try not to pose any risk to the contenders asked for exactly what he received in the race as you have pretty much acknowledged, and I don’t see how it is ever illegitimate to race legally for position; if he was Lorenzo’s out of contention team mate he would have been expected to race Rossi in that manner, and there is footage of Colin Edwards doing on Rossi’s behalf. Rossi himself has raced others in the same fashion, LS08 and Motegi 2010 being examples; after the latter race Lorenzo was criticised by Rossi fans and Rossi actually said he was entitled to race him.
Bottom line is that taking MM out at Sepang very likely allowed Rossi to finish 3rd rather than 4th, and at no time later in the race did he show signs of having the pace of the leading 2 riders just as he showed no signs of having the pace to finish higher than 4th at Valencia.