First impression: Brian was and is a genius arranger with a very unique, specific, and identifiable sound to his work. When he had the Beach Boys vocals as his instruments, I believe he realized he had one of the most unique vocal blends of the time, specifically up to 1967. That vocal sound was his and the band's trademark, his "fastball" pitch that no one else had.
With that in mind, as he worked up instrumental tracks in his mind and in the studio, I believe he either consciously or subconsciously left enough musical and sonic room/space in his arrangements where he could sit the vocal blend on top as the featured instrument and texture of his productions with the BB's. As inventive and creative as his instrumental charts were, he had to be thinking of that sonic trademark coming most prominent in the vocals, again those vocals were the fastball pitch that no one else's records had.
In that way I think the concept of using instruments as vocals would defeat the whole purpose of his records, which again was to deliver the vocal blend listeners liked and expected. So perhaps a few instances where the lines were crossed may have been deliberate, but overall if it did happen it may have been more coincidental than deliberate, where maybe an instrument's line or pitch blended in with a vocal line.
But if your main selling point is a vocal blend, as a producer and arranger you wouldn't purposely detract from that by having instruments replace or act as vocals.
Just my 2 cents.
