I'm a linux user and have always had success exporting to Windows and Mac using the Godot Engine. So, don't sweat it. It will more than likely work.
If you do an HTML5 export, I would suggest either testing it locally somehow, or uploading it early to itch.io and making sure it works. I've had interesting surprises in the past where something didn't work quite right, so now I always test it in the browser. You don't even have to make it public on itch if you don't want people to see it before submitting it to the jam. you'll still be able to test it yourself.
Also, a reminder, you MUST use the Godot Engine for this jam.