On OK Computer-era performances of Planet Telex, Jonny used his Electro-Harmonix Small Stone V2 and Marshall Shredmaster while playing all guitar parts. During the choruses and second verse, he actually adjusts the Small Stone’s “rate” knob with his foot while playing, as you can read about in the article on Planet Telex Live Arrangements.
Jonny used that Small Stone technique during the choruses and second verse of every performance of Planet Telex from its live premiere in 1995 through the 2012 tour. Part of why it sounds different to you during the 90s could be that Jonny may have set his Shredmaster slightly differently back then (maybe a bit more gain?), or that he was using a different version Small Stone at the time, or that his guitar was mixed and EQ’d slightly differently on those tours, or some combination of factors.

A photo of Jonny reaching to adjust one of his modulation pedals during a show in the late-90s – maybe his Small Stone V2?