Pantani's performance in Plateau de Beille 98 and Alpe D'Huez (95 and 97) are extremely different. It seems that people only look at the time without knowing the details of that climb.
Pantani wasn't supposed to even participate at the 1998 Tour de France. The president of Mercatone Uno suddenly died and in order to honor him Pantani decided to start at the TdF as well, after the legendary battle during the Giro vs Tonkov. To reiterate this, Pantani specifically trained to reach his absolute peak during the 1998 Giro.
His form was absolutely terrible in the first week of the TdF. He lost 48s in only 5.6km in the Prologue
Plateau de Beille 98 is one of the "worst" Pantani performance if we only count his wins. He was far from his best days, and even Cassani (Italian commentator back then) highlighted this during the stage, saying multiple times that Pantani wasn't doing anything special. It's actually insane that his record lasted so many years.
He won because Jan Ullrich was struggling as well. In fact, he completely cracked in stage 15 losing an insane amount of time.
Moreover, we should also take into account that Pantani had a very serious injury in 1995. He needed years of hard work to come back at his best level, especially in terms of consistency.
Having said that, Pantani is by far the best pure climber of cycling modern era.