Most companies that have this agreement in place also have a similar agreement when joining the company that if you forego signing the exit agreement, you forego any outstanding debts owed to you by the company.
This sounds a bit illogical, but I'm not a lawyer. Another poster said it wasn't the practice at all in his years of experience, so maybe your experience does not generalize well.
You're also making an assumption that such a contract was made in this case - and it clearly wasn't, since the Miso people acknowledged their mistake here. So the guy absolutely deserves the bonus payout, even if he didn't submit the administrative form to claim it while he was still there.
There's also the question of labor laws. I bet this is considered wages under the law and probably impossible to sign away.