Keith, the algorithm for auto-excluding partial shots is specifically intended for chips, bump-and-runs, etc. If you track your shots during a round and hit for example a 6i from the fringe, you will notice the shot will be auto-excluded from distance statistics. Here's an article that explains how to check that and how to manually include or exclude a shot from distance stats. The alternative solution you described with designating a special CPFF club would also work, but it isn't strictly necessary.
Hope this helps, do let us know if you have any questions.