I agree with most of this. You can certainly come up with plausible reasons as to why Pog was beaten so soundly but I think it obscures the likely reality that he was never going to win this Tour no matter what.
Race-wise, JV has about the same experience as Pog even if he's slightly older and compared to Pog and a bunch of this new generation, he wasn't an early bloomer. We've seen substantial improvement from him every year and I'm sure no one actually thought he had reached his peak when he won the Tour last year, despite beating the best rider on the planet. He seemed like he was right in the middle of his improvement curve then and it seems like he's just now starting to tap into his full potential. Honestly, it feels a little Froome-ish to me.
I still think Pog is the best rider in the world but I also think Jonas is just a better GT rider at this point, partially because GT racing suits him to a T. Not saying it doesn't suit Pog but really, just about anything suits Pog - he's that good and that well-rounded. But everything about JV screams GT rider and that's 3 years in a row he's beaten Pog in a 3rd week TT - I don't think that's a coincidence. Of course I also wouldn't write Pogacar off or be too shocked if another youngster or 2 threw himself into the ring but we could be in for another period of dominance.