We know most game jams are okay with bug fixes post deadline, so long as it doesn't change gameplay drastically. So would our team be able to fix a few of our discovered bugs, or should this be listed as a separate "post-submission" entry ?

I suggest adding it as a separate "fixed" version, and letting users know it's a fixed version, rather than overwriting the current jam version. They'd both be on the game page, so users can choose which they'd prefer to play/rate.