Nadal has 20 majors, and it's quite clear that injuries were what prevented him from winning many more. He was dealing with tendinitis when he lost to Soderling in the 2009 French Open. Also, who can forget the 2014 Aussie final where he was about to dumpster Wawrinka, only for his back to suddenly flare up and basically cripple him for the rest of the match.
"Single discipline"...? He won 5 majors on hardcourt and 2 on grass, in addition to 13 on clay. Fed has just one on clay, and there's no chance in hell he wins that if Rafa is 100% for that tournament. It's pretty telling that Rafa has beaten Fed in a Wimbledon final, but Fed has never beaten Rafa in a French Open. Is it better to be absolutely dominant on one court type and very good on the other two, or be very good on two and mediocre on the third?
What's more, Rafa's win % in majors matches is 87.9, compared to Djoker's 86.8 and Fed's 86.0. Also, in head to head matchups, Nadal leads Fed 24-16 (10-4 in grand slams).
Not only is it arguable that Nadal has overtaken Fed as the tennis GOAT, I would say that it's very clear that he has. A lot of Fed's majors were won during a period of time when Sampras had retired, Agassi was on the decline, Nadal had not entered his prime yet and Djokovic wasn't on the scene yet. Nadal, on the other hand, won all of his majors while in direct competition with Fed and Djoker.
The only real question is whether or not Novak surpasses Rafa before all is said and done, but we'll see. Remember that Novak is only one year younger than Rafa (albeit has had far fewer injures than Rafa).