Of course its debatable as anything can happen on any given day, but the point is even the Fed fans were picking Nole before the match and clearly there was a reason for that.
On a slower court Fed struggles very hard to beat Nole. In fact since 2011+ the only slow court wins Fed has had over Nole were at 2014 MC (where Nole was injured) and 2011 RG (where Fed played one of the greatest clay court matches of his life). Go look at RG 2012, WTF 2012, and AO 2011 for examples of matches on slow courts when Nole is playing at his best. The count 8-0 Nole in sets.
Nole beat that same Wawrinka (who had just crushed Berdych the match before 1 and 1) by a score of 3 and 0 and also gave that same Kei who was testing him both a bagel and breadstick.
I don't think you're being quite fair in your analysis. What does AO and much less, RG, have to do with the WTF?
And said WTF match, which you use to show what happens, when Djoko plays great vs. Fed on this court (2-0 in sets as part of your 8-0 in sets on slow courts argument) was a close a match as they come.
Fed led the first set 3-0, was close to get a 4-0 iirc, and the TB was very close as well with Novak eventually winning it 8-6.
In the second, Fed was up a break again, failing to consolidate with the 2nd break, serving for the match at 5-3, before Novak came roaring back winning it 7-5 after making some stunning returns at 125 mph bombs down the T.
In total points won, Novak led Fed by just one (96-95), yet you simply state it as another 2 sets victory.
As for you talking about the 'same Wawa', I mean, seriously? Wawa is the streakiest of players. He can play great one day and suck the next. He was fairly good for a set vs. Nole and not good at all in the next. Just because Nole beat him much easier than Fed, doesn't equate to Nole = easy win over Fed (as I'm sure you know).
And the same Kei, who was testing who? Fed (2 and 3??)? You mention the breadstick and the bagel from Nole, but you forget the lost set. A bit dishonest, don't you think?
You very well know that if Nishi had gotten one of his BP's at the start of the 3rd, there's no saying whether Djoko would have remained shell-shocked or not (oods are - Nishi would have gone down a level eventually as he seemed nervous the minute he got a chance to win, but again - we don't know. The 3rd set was more about Nishi not being there than Novak playing great. He played very great in the first though).
All in all, yes, Nole would have been the favorite on Sunday even against a healthy Fed, because of his form and because of the court. But as you yourself pointed out and as their matches throughout the years show, their matches are usually very close and hard to call.