I am not saying Froome is clean, he definitely sits at the top of the segment between definitely not doped and definitely doped. However, 3-6 minutes is not a huge lead when you still have 5 HC climbs left in the tour and you are bound to lose fitness, not improving it or keeping it if you are clean. I suspect a huge attack will come on Ventoux when they reach 1200-1400m and I am positive one will come as they reach the summit of Le Alpe the first time and on the Glandon at around 1600m. If Froome is doped then Ventoux ascent records (minus the time trials) are in peril.
VO2 requirements at sea level and altitude are two entirely different things. I don't try to confuse VO2 and power outputs, some guys are maxed on muscle power output but not on VO2 at sea level primarily because they don't do enough lowland training. They need a steep hill, crazy gear ratios, and altitude to bring them into balance because that happens to be a substansial portion of their training.