I agree with you that it's rare, but in scenarios that involve very high-ticket type players, it does sometimes play a factor. Fielder is the absolute epitome of a owner stepping in and pointing out exactly what he wants. Anyone can look back at his signing, and you'll remember clearly that the Tigers came out of the blue, and it was soon discovered that it was because Illitch wanted to make it happen.
Just the way it was marketed, and the way Beeston spoke about it (especially his quotes in Davidi's book), it seemed like there was a higher involvement in the move. I'm not saying AA is completely innocent for those moves, because that's the same offseason where he made that atrocious Gomes for Rogers move, but I don't pin it completely on him either.
Regardless, all of this stuff is in the past, and he's on absolute fire right now, so what's done is done and we should all revel and enjoy what's going on now.