Yeah, good point about using a long enough siphon hose, I do use a length of tubing that does circle the bottom, but to me the act of exposing beer to a new (relatively) oxygen rich environment in a secondary and the resulting turbulence exposing the surface of the beer to the air I just can't help but transfer while the beer is still opaque with yeast. I still end up with a nice layer of yeast falling out of suspension so no worries of stuck ferments. If I were to estimate how finished fermenting my beer is, I would say 90% done.
Again, probably one of those techniques that it probably doesn't matter, or is insignificant to such a degree as opposed to other factors.
Your mileage may vary