Yep, we all face the same problem.
Get as many city-pairs and passengers as possible on your waiver and send a fax to TSA with additional details in case of last minute flight not covered by your current waiver.
You won't get a reply from them quickly enough but that's the only way I can think of. At least you have advised them, better than nothing.
Penalties I don't know but I wouldn't mess with those guys.
We are now obliged to spend fortunes in lawyers fees in order to find our way through their never ending requirements and approvals.
US operators don't have indeed this kind of problems here, it's more than unfair as we can't offer same flexibility to our customers.