(I am the author of the article) You are correct that he wasn't clean early in his career. He admitted to first using a banned substance in 1993, which was the year he won the World Championship, and I recall the 2012 investigation had testimony of his using drugs on Motorola in 1994. I also don't think there's any convincing evidence he actually lost much weight in 98 when he had his first high GT finish at the Vuelta. There are probably many possible reasons for how he transformed into a grand tour contender in 1998 -- from "dialing it in" to completely changing the strategy, but I haven't seen any agreed upon theory.