Interesting that nobody has mentioned Ullrich in 1997 yet. Because honestly that's what this reminds me of. That year he finished 2nd in the opening prologue, taking 42 seconds on the eventual runner up Virenque. Then in stage 9 (after 8 straight sprint stages, as the prologue didn't count as a stage back then) and finishing with Pantani and Virenque in the first hilly stage he took 1:08 on both of them in stage 10.
Which doesn't sound as impressive, but he took 2:01 on Casagrande in 4th and 3:23 on last year's winner Riis in 5th. He also followed that up by taking 3:04 on everyone in the stage 12 hilly time trial. At that point he was 5:42 ahead of Virenque in 2nd and 8:00 ahead of Olano in 3rd, with most of that time coming in 2 stages. He ended winning by 9:09 over Virenque and 14:03 ahead of Pantani in 3rd. And if I remember correctly, he never really tried to do all that much after stage 12.
The big difference is that there were some other riders well ahead of the pack (well that and a lot of clinic stuff back then that has been well documented by now). Meanwhile Carapaz finished in a group that had 3 riders in it that never finished top 15 in a grand tour (Vingegaard, Lutsenko and O'Connor), another 2 that never made a podium (Gaudu and Bilbao), 2 more with only a single podium (Mas and Kelderman) and Urán, who finished 2nd in three Grand Tours but is also 34 and finished 7th and 8th the last two years.
While Pogačar might well have dropped a fully healthy Roglič, or Bernal if he had been in this Tour, I doubt he takes the 3:25 he took on the group of Carapaz today. Not just because of the quality but also because I can't help but feel that some riders in that group could have done better but resigned themselves to racing for the podium.
I also wonder what role the weather played, as that does tend to exaggerated the differences and some riders don't deal with that as well. Which also brings me back to Bernal not being here, because he showed in the Giro that he can deal with bad weather pretty damn well.