Fender has told me that they are not going to continue this practice on their brand new models. The original Fender guitars were built like the one on the left and most of the ones built today are built like the one on the right. Many people believe that the reason the original guitars sound so good, is because the pickups are not attached to the wood. They actually hang in those pre tuned cavities. There are also people that believe that the magnetic field interference are reduced by the separate cavities.
Fender takes the less costly approach and routes out a swimming pool in the middle of the guitar.
This makes construction easier and a lot less expensive. Some people actually argue that the quality of the wood is not that important on Stratocasters. Because the pickups aren't attached to the wood but actually suspended and spring loaded to a plastic pickguard. I personally don't believe there is anything wrong with this method of mounting pickups. I personally prefer to mount them solidly to wood .