The regular CBet Flop includes all preflop pot sizes, if you want to see the specific 3bet and not 3bet pot breakdown you need to use those specific stats. The general "Bet River" stat is for all river bets regardless of anything else that happened before - cbets are included as are any other chances you had to bet. It basically ignores everything else that happened in the hand, and then there are more specific river bet type stats that look at more specific situations.
See
this guide for the basics on custom statistics creation and
this guide for a deeper walkthrough. The latter was written for PT3 but the techniques all apply to PT4, the interface is just slightly different.