I agree. Block time should be used, not flight time. That's the metric that real airlines use. While airborne time is measured and estimated (remember, it's just an estimate), it's not what's used to determine whether a flight is on time or not. Departure from the gate, and arrival to the gate is. This would also make the user experience easier as we wouldn't have to calculate the estimated taxi time, estimated boarding time, and other factors for the "time until departure" setup.
Often, tailwinds might make me very early, especially on longer flights. If I'm 1 minute over my estimated flying time, PACX will mark it as late, even though I'm still 20 minutes ahead of the scheduled arrival time at the gate.