Nadal's record against Fed is because Fed makes the finals on his bad surface much more often than Nadal makes the final on his bad surfaces. The losses on clay to Nadal are a testament to Fed's greatness on all surfaces, he just ran into possibly the best clay court player of all time when he makes those French finals.
To me it is like having two football kickers. One of the kickers is a specialist for kicks over 55 yards and dominates every other kicker at that distance. He is still a great kicker below 55 yards but not elite at all. Meanwhile another kicker is the greatest on all the other distances and second best when he runs into the specialist kicker for the kicks over 55. There isn't much doubt who the better kicker is, but if a majority of the kick contests between the two kickers occur over 55 yards, then the specialist is going to have a better kicking record than the overall better kicker.
To me it is like having two football kickers. One of the kickers is a specialist for kicks over 55 yards and dominates every other kicker at that distance. He is still a great kicker below 55 yards but not elite at all. Meanwhile another kicker is the greatest on all the other distances and second best when he runs into the specialist kicker for the kicks over 55. There isn't much doubt who the better kicker is, but if a majority of the kick contests between the two kickers occur over 55 yards, then the specialist is going to have a better kicking record than the overall better kicker.