I use to do this with paper and pencil so I understand the tradition of a cutoff time. But then again, one of the reasons why I originally wrote the online app was to avoid having to deal with the last minute rush
In any case, it probably could be made into a configurable option, but I haven't gotten to it. The link kamokid pointed out will do the trick.
The second chance survivor pool is another popular request that I haven't gotten around too. If you want a quick an dirty solution, set up a separate installation of the pool. As far as running into the playoffs, it's certainly possible but the big complication is the use each team once rule.
Not a bad idea on the overall, but again it gets really complicated from a coding standpoint. Mainly because all the post season pools are optional so you have a number of possible combinations to account for.
Interesting take on a Super Bowl pool. How do you decide who picks in what order? Or is it at random?