So then the prevailing educated opinion of the clinic is that UAE/Pogacar came up with some kind of substance or protocol which enabled him to beat the snot out of all the clean or inadequately doped competition, but then Jumbo/Vingegaard developed something that totally trumped whatever Pogacar was on, and that even though no one else seems to be able to avail themselves of any of this rocket fuel they will all keep quiet because....omerta. Is that about right?
I think that's always been the personal hell of Clinic denizens that there is so much we have to speculate, I don't know anyone can really tell. The only things factual (or as close to factual) are that overall peloton performances have seemingly jumped up again from 2020 and that a few riders (including Vingegaard and Pogacar on the Tour) are clocking insane times warranting reasonable suspicion.
Beyond that... Is it that Jumbo, UAE or Sky have access to supposed new methods ? Pharma, genetics, motor ? Or that they're better at it ? Willing to supercharge more ? Are only charging key riders to avoid being too conspicuous ? That they are actively or passively protected and as such have more leeway ? I don't think one can provide a definitive answer to that.
The best I can offer is that we know from past cases that teams can be more crooked than others (because of the history and legacy of people involved).
That the teams most often scrutinized (both for outstanding performances of leaders and very high floor for the whole roster) here generally are among the wealthiest of the WT so theoretically could have access to better implementation of PED.
That even with systematic team level doping, there's still a hierarchy of riders.
That doping specialists learnt a long time ago you need to pace it for a variety of reasons including not raising too many red flags.
That some riders respond better to enhancement than others.
I'll add (and some recent musings may confirm that) that it's not too farfetched that the peloton will not rock the boat so long that (alleged) dopers are not killing all competition too blatantly.
From there, I feel the simplest, less complex explanation for the ITT results if we assume cheating is involved :
Pog, Vingo and their respective teams both identified some time before hand it would be a crucial day and overdid it way past the target because they were neck to neck in GC and probably assumed the other would pull all stops. Considering Pogacar bonking the day after, possibly suboptimal prep and general fatigue, it was probably his all-in moment anyway.
Overall they both dominated the Tour head and shoulders and there was quickly no doubt on the top 2 (bar Pog completely collapsing until Paris) but both of them being so close help hid a little just how far ahead they are (and though it was an exciting tour in the mountains, you didn't get -IMO- a crazy solo perf like Armstrong at Sestrières 1999).
Maybe their teams have access to better stuff. Or just dosed them as far as they could.
Probably that Pogacar and Vingegaard, if cheating, do respond better to it than most riders on top of their natural talent or physical idiosyncrasies.
My 2 cents of the most reasonable scenario not involving super secret sauce or mass active collusion outside the teams.