I see that now that the community rating period is over, uploading files to itch has been unlocked. Does this mean we're allowed to make any updates to our game? If so, will the moderators/judges play the original version or the updated version? If the former, then how would they even access the older build? Look through my GitHub commit history and compile from the older build? If so, then why even unlock uploads in the first place?

You can always keep the older build available on itch and rename it "Jam build" and continue to upload updates to your game.