They published a similar list in 2003 and Brian was, interestingly, #39 in that one.
Since neither include Mike Oldfield, who could play circles around a lot if their entries, and because Rolling Stone has made its reputation on pretending to know what its talking about (with questionable results), I'm inclined to disregard any such lists.
These things can never be comprehensive, as it cannot take into account every recorded performance and qualify the sum total of a career. Nor can it ever truly gauge the quantity of influence, partly because influences are always changing, as are society's standards.
Besides, why make it a competition? The only thing, in my opinion, that matters is serving the needs of the song.