Yes, a flow meter can be installed in a valve box after the backflow preventer. It will give you a total. Here is an example: Hunter Flow Meter
There are others on the market. The main flow meter manufacturers are Badger and McCrometer. They manufacture meters for irrigation manufacturers. It would be cost prohibitive to install a flow meter on every zone.
These are generally not cheap, but they are accurate. You will need to use Schedule 80 fittings to connect PVC to metal.