I think at this point, it's safest to assume that all the top riders are doping. Pog and JV are playing another sport from the rest of the GC riders. Then you have WVA, who did an absolutely insane pull yesterday, eventually riding away from Pog, after killing himself for hours pulling the breakaway.
That being said, I didn't see this TdF as JV being suddenly better than Pog. The way I saw it, Pog maybe got a little cocky on Granon, or maybe he genuinely had a very very rare off day. JV was able to take big advantage on that one day.
All the other days of this Tour, it's looked like Pog was at least as good as JV, or maybe better. Put it this way, say Pog had a 10 second lead on JV after Granon. The races in the Pyrenees would have looked totally different. Instead of trying constant attacks, Pog could have ridden defensively, saved all his energy, and forced JV to try to attack. JV doesn't have the burst to attack uphill like Pog does, so I don't think JV could have ever made up that time.
If Pog hadn't attacked 5 times on the second climb yesterday, he surely would have been able to best JV on the final climb.
In short, I think if Pog didn't have one bad day on Granon, he would have won this Tour again, fairly easily. So I'm not convinced that JV is suddenly going to be the new best rider, or even routine competition for Pog. I think he was in the right place at the right time in this Tour.