Can only speak for myself but I think it's a lot more mundane than that. Overload, progression, specificity and rest are the well established principles of training. Doping amplifies them, but doesn't remove them.
I assume Jumbo and UAE have more or less equally potent prep regimes, but obviously cannot substantiate on that.
Keep in mind though that absent Vingo, and Pog both stomps the field and does not collapse himself.
On top of that I think:
1) Vingo's physical constitution and mindset, whichever way they are attained, are better suited to GC racing. His prep was also very good and specific.
2) Pog lost a huge chunk of training volume after the crash. One can use turbo riding as a substitute to an extent, but in the end 6hr days of climbing at altitude win. This is how you build the required base in a specific manner.
Also if he was on a heavy weight loss regime after the classics, it probably doesn't hel. Unless one goes full Sky and lets TUE-ed intramuscular kenacort just eat the excess away.
Pog was brutally dropped on the Marie Blanque, then suddenly gained the capacity to occasionally drop Vingo and rival Mr. Pantani's climb times; but, in short order he also lost the capacity to drop his rival. To me it was fairly straightforward to conclude he was running out of base. I assumed he would pull a monster performance in the ITT and collapse on the Loze, which he did. Only Vingo completely stole his thunder with his bemusing stunt.
3) The two may have deployed their resources during the tour at different times. This refers to both the clinical stuff (good ol' blood bags) and the riders' capacities to recover from going into the red. The user extinction in particular has stressed that given the circumstances, Pog was effed trying to follow Vingo no matter what, and I think he is onto something. Threshold power level relative to rider weight and especially the capacity to repeat efforts at this level is decisive in the immediate sense. Day to day recovery is decisive in the mid-term.
Of course their prep regimes may also greatly differ, but IMHO you don't need this premise to explain what we saw regarding JV and Pog's relative performance difference. As for absolute levels, it's anyone's guess.
It's an aerobic sport, dammit, and base rules.