I wouldn't care one way or the other.
The player finishing in first would have gotten $90 less if this rule was in place, but he missed two tournaments, the buyins for which were likely $40 each, so the difference is really $10. $5 for second place and third place loses less than the two missed events would have cost him. Not much difference for regulars, but if someone is comfortable with their points and sitting on the fence for Event 11, this rule might get them to come out.
Azcat is certain that a part-time player will never make the Top 9 and therefore sit in the Championship (esp. now that there is no Qualifier tournament). I think Kevin A. could cash in 5 events, winning 3 and make the final 9. Last year, it only took 30.48 points to hit 9th place. Kevin subbed one event and already earned 9.19 points (and it could have been higher if he would have played it out instead of chopping heads up).
I think technically it would be a rake. Isn't "all" buy in money supposed to be paid out?
Setting aside the issue of whether the leftover constitutes a rake, what are your thoughts?