He's definitely using p90s with the jazzmaster. It really takes a good sound system or headphones to clearly hear all the harmonics of that fuzzed out sound, but like i said the 'sound' has been his main goal his whole life. Similar to Kevin Shields, with ridiculous walls of fuzz. I really doubt you can get this sound from an LP. I am big on tone too and i like tones that are on the opposite end of the spectrum as well, but to hear overwhelming fuzz with definition is pretty rare I think.
Autolux and My Bloody Valentine have similar things going on.
If you ever watched Sonic Youth play, you notice they are all extremely articulate with picking style and positioning over the neck, to get ultra rich smooth harmonics. This is to ensure every strum has the exact tone that he's looking for in it's place with the mix. He studied extensively on the topic of tone and getting multiple guitars and bass to mesh into a smooth singular entity and i think he does the grunge sound well. Not my favorite tone but awesome nonetheless.
Clean, it sounds like the strings are going right through your head. THen around 2 minutes, when everything is fuzzed i find it amazing that you can still keep track of who is playing which parts. That's just really good sound production.
But yeah, acoustic performance of this type of music is total garbage, i think it's all about the sound of the electric guitars more than the songwriting.