A short ITT would definitely make a difference. You can appreciate it from the red line in Nibs' analysis. The line goes up as time goes down, because more power can be put out for a shorter period of time. The line is in fact an estimate based on what he was known to put out in one sustained climb of around forty minutes.
However, I assume Vayer would have factored that in. He would either have to make all his power estimates from relatively sustained climbs, or use a projection like that red line to estimate what sustained power would be based on power output for shorter intervals.
If Hinault had a power output of 6.4 watts/kg for a sustained climb, around 40 min, then the only thing available at that time that would explain it would be blood transfusion. But there is no evidence that he did that, and if he did, one would expect he would do it at other times, as well.
I haven't read the book, of course, but if he's claiming Hinault did 6.4 watts/kg, then there is almost certainly something wrong with his calculations. Most likely he used too short an interval, and if he did, then many of his other estimates are probably wrong, too. But again, it seems hard to believe that Vayer would make a simple mistake like that.
Edit: Where did the 6.4 watts/kg come from? According to what I've seen, Hinault was classified as yellow. This would mean > 5.85 watts/kg. This I think is believable without EPO. Remember there is considerable variation in on the road estimates due to weather conditions. E.g., Hinault could have had a tail wind on that climb.