So most tournaments that would lend themselves to participants not playing 50% of the required games are larger expo's, or leagues that last many weeks/months. This isn't much of a worry for those 'one night setup and go' tournaments.
Ultimately the IFPA will be looking for the number of players tied to our "Player Count" field in our database, which is the total number of players in the results that were submitted. Any over payments will be dealt with between myself and the TD. Refunds won't be a problem, but I find that most TD's run more than one event, so we can always apply that overpayment to the next event. I already know of some TD's that plan on just advancing me $100 at a time, working that balance off, and then reloading whenever it's appropriate.