really surprised it doesn't sound off to you. these sorts of discussions can frustrate me, because even tho i know music theory now, i've had an ear for this stuff since childhood, before i received any music training. it was only later after learning theory that i was able to put words to many of the things that i had previously felt about music.
anyway, i sat down with my guitar and the tabs and really tried to figure out what it is about the transition that sounds so off to me. it took me a minute, because it wasn't until i paid attention to what was going on with the bass that i realized what was up. the chorus to Opiate sounds very "major" to me. tool largely plays out of D Dorian or D Aeolian or modes that are one or two notes off from those. i looked at the guitar tabs, pretty standard power chord progression, B5 -> D5 -> E5 -> F5. that wouldn't sound as "major" as i was hearing tho, that third chord of the riff definitely sounded major, and sure enough the bass is playing a G# there, making an E Maj tonality instead of the E Min tonality you'd expect if you were to extend that E5 out to the third it would be implied to have by all the surrounding notes. this gives the chorus to Opiate a pretty different feel that the usual Tool D Dorian grooves. they switch back to regular D Dorian for the bit they added to the song in the middle. so yeah, it's not what the guitar is doing, but what the bass is doing that makes it end up sounding so ham fisted to me.
edit -- probably more appropriate to call it B Locrian? idk, it's been a long time since i've had to write any of this stuff down, my head is starting to hurt haha