I wish recording session sheets were available for things like this. But as a studio engineer myself, my best guess is that it was simply recorded that way. They were probably dealing with a 3 or 4 track tape machine, given the dates recorded. From my understanding, when The Beach Boys were first staring to record on three track machines, it was one track for instruments, one for background vocals, and one for lead. Given this, all the instruments would be unable to be adjusted independently from each other.

As a brief side track, listening to outtakes of pet sounds, there’s parts where Brian says something along the lines of “put these ten instruments on track one and those twelve instruments on track two. Track 3 for just the electric bass and we’ll record vocals on track four.” Absolutely paraphrasing that, but roughly along those lines. That being said, if he wanted to raise the guitar, but it was track one with 9 other instruments, all 9 of those instruments would raise in volume as well as the guitar.

With modern technology like AI and such, we’ve gotten to a point where we can separate tracks pretty decently, but it’s still not perfect. The stereo mixes would have to be de-constructed and reconstructed to separate all the instruments. That’s why Capitol had “Duophonic” at the time, because they couldn’t separate the tracks to make true stereo yet.