There are too many Tom's involved in this discussion.
Tom Paul,
I believe I sent you an analysis of what the effect of removing bunkers from the rules would be a couple of years ago. I have it at home and will try to post it tonight.
To both Tom Paul and Tom Doak, while Rule 13-2 does prohibit improving your lie and would protect from most egregious acts, there are exceptions that would allow some improvements.
The first is that you can ground your club lightly in sandy areas that are through the green. Probably not a big improvement from that. The second is that in making the back swing for a stroke the player could knock over a pile of sand that was blocking his forward stroke. This could make a pretty big difference for some shots.
I believe that declaring areas that meet the definition of a bunker as through the green actually waives a rule of golf and is therefore not allowed. They could have more easily taken the opposite tack and declared all sandy areas as bunkers.
Tom Roewer, while the definition of a bunker doesn't include the word rake, the phrase "a prepared area of ground" implies that it was the intention of the the architect or the superintendent that the area be a bunker when they designed or prepared it as such. Therefore, if an area has been raked or otherwise manicured, it should be considered a bunker.
At Sea Island for the 2004 US Mid-Amateur, we said that if an area had been raked it was a bunker. If not, it wasn't. There were many areas where an area had been raked and connected to areas that hadn't and there were no rules incidents with regards to confusion. In general, we told the players that they should always use caution and act as if the area was a bunker.
Probably the biggest problem area at Pacific Dunes is the hillside to the right of the 13th green. As I recall, the flat area at the bottom is raked and maintained as a bunker, while the rest isn't. It shouldn't be too hard to determine where one starts and the other ends.