Rip claims that all lifters reach the scap spine over bar position eventually, so why not start there, because it's more efficient - he wants a straight bar path for that same idea of efficiency.
The problem is that it's simply not true that the bar always ends up in this position. Go watch some video (of weightlifters, not crossfitters or other athletes) and you'll see very clearly and very quickly that this is simply not the case.
Also, "efficiency" is a concept that requires a lot of qualification. You can't consider the body and bar as this whole unit and just plug in 2 numbers to calculate. You have to consider the relative contributions of various muscles, the effectiveness of certain body positions, etc. It's not that simple of a movement.
The body is not a forklift - just because a straight bar path is "efficient", doesn't mean it's a good idea. There's a lot more to a snatch or clean than the efficiency of the bar path. Have you considered the requirements of body position to achieve a vertical bar path? It doesn't work. Besides, the "S" pull doesn't actually look that much like an S - it's damn close to vertical when done correctly, with the slight horizontal movement that's quite simply necessary to perform lifts with the weights at elite levels.
And remember, when you say over the bar - even with this more upright start, you'll be over the bar initially - the arms being vertical will place the shoulders slightly ahead of the bar. It's an issue of degree - it's not like we're behind the bar.