The 3-0 is pretty balanced by this point.
Yes Fed was near 33, 34 & 38 but he had ample chances in the two 5 setters losing 4-6 and 12-13 in the final set. I mean with 2019 specifically going 0-3 in tiebreaks and having double match point. Like you can't turn around and use the age argument all of a sudden because he freaking choked those matches.
Anyhow, gotta look at the draws. If we're just looking at QF-SF:
Federer
Schalken-Roddick-Phillippousiss
Hewitt-Grosjean-Roddick
Gonzalez-Hewitt-Roddick
Ancic-Bjorkman-Nadal
Ferrero-Gasquet-Nadal
Karlovic-Haas-Roddick
Youzhny-Djokovic-Murray
Raonic-Berdych-Cilic
Djokovic
Tomic-Tsonga-Nadal
Cilic-Dimitrov-Federer
Cilic-Gasquet-Federer
Nishikori-Nadal-Anderson
Goffin-Agut-Federer
Fucsovics-Shapovalov-Berrettini
With the bolded aquamarine being cross-overs. For Fed to have the upper hand outside of the 2 extra Slams, we need to look at the odd other opponents:
Grosjean, Schalken, Phillippousiss, Bjorkman, Youzhny, Raonic, Berdych, Karlovic, Haas, Ferrero, Ancic, Gonzalez
vs.
Tomic, Tsonga, Dimitrov, Nishikori, Anderson, Goffin, Agut, Fucsovics, Shapovalov, Berrettini
I would argue Fed's toughest roads were 04-06 and 2012, and none of those would I call anywhere near Edberg92 level of difficulty. In every one of those cases you still had 1 of those final 3 opponents being relatively easy and the toughest one being limited, like 06 with Nadal or 12 with Murray despite that being his prime-peak form. Novak on the flip side has 2011 & 2014 being at least equal to Fed's toughest runs of course Tomic is a punchline now for that particular tournament he was probably at his best but Tsonga and Nadal were both very high level for that time. I would still err towards 2014 given Cilic and Federer's form while Dimitrov wasn't exactly a gift match just ultimately not dangerous for defeat (kind of like Shapovalov now).
But historically, I'd still say Fed is above Novak with the 2 gap in titles and 3 additional finals on top of that. It's just too much but given Novak's age I do expect him to surpass Fed as the ultimate champion even if Fed maintains the presence being a 12 time finalist.