Just to add to the conversation... FWIW, I remember reading around the time the WOTS comp was being released that the album version was ultimately used on the comp because the tape and/or fidelity (?) of the existing single mix wasn't in as good of condition as the album version. Anybody recall that?
IIRC it was also the reason why the LP version appears on the '93 box.
Old thread, but thought I'd weigh in.
I just put together a one-CD comp entirely drawn from the 1972-73 period for my enjoyment while driving and for the benefit of some friends of mine (who need to know that the Beach Boys are more than Surfin' USA).
I used the Brother Years single mix of California Saga and there was a notable drop off in sound quality from the tracks that preceded it (all drawn from the 2000 remasters and MiC). I just replaced it with the album cut which, to my ears, has a much fuller and more pleasant sound. The Brother Years mix is harsh sounding and compressed to the degree that the cymbals and "s" sounds seem unnatural.
Until better tapes show up for the single mix, I've got to go with the album cut as my preferred version.