So, basically, the company can dictate the exact debts in its exit agreement? And if you disagree, you forego all claims anyway?

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.