In general, I'd say don't make any changes to the the game on itch.io until after the voting period ends. If it's a bug that seriously affects/prevents playability (or adding you're support for another platform), I'd say go for it. I'd recommend leaving a note on the itch.io page saying what was updated and why. Since the code isn't being judged, you're welcome to make whatever changes to the repository you like :)
Thanks for the question; this is a good one to add to the FAQ...
Cheers,
Lee