Federer has not done any better than Murray in the last 6 slams. He is cleaning up in the MM tournaments though.
Masters are not MM tourneys.
About the Slams, you are 100% right! If you take into account that Fed's results in Slams those two years are considered disappointing, and Murray has been good (for him) at Slams since the start of 2011, you can see how getting ahead of these guys is so different from making an upset. One great performance isn't gonna cut it, and nobody is capable of being better than them for a long period of time.