Well, no one knows for certain, but based on what Billy and Flood have said, Billy loved the Big Muff tone he got on SD, but had trouble with the Muffs when they toured - they compete with the bass low end and is hard to hear live. He dropped the pedals and switched switched to using a Mesa Boogie Strategy power amp, a Marshal JMP-1 preamp, and an Alesis 3630 compressor to drive more gain into the Marshall for the live fuzz/overdrive sounds.
He got a similar low end fuzz tone like the Muff with that setup. When they went into the studio for Mellon Collie he had the same setup, but Billy also has just about every vintage fuzz and modulation pedal known to man, so he uses lots of different stuff on each song. Lots of old EHX pedals. You hear ring modulators, the Micro Synth, Fender Blender, phasers, and kinds of stuff, not just one pedal. It is different on every song.
Most of the rhythm stuff seems to be the preamp distortions, but I still hear the Muff on a few tracks, like JellyBelly and Here is No Why. The rhytm tracks are multi tracked numerous times, so you can’t quite get that exact sound from a single pedal either. I don’t hear the Muff used for any of those solos, but with all the modulation Billy uses you could use any number of fuzz pedals with the same modulation effects and get similar sounds.