Do I need a re-entry permit if I have a visa-free entry and a 30-day extension?

As you entered on a visa-exempt, you can just forget about that part.

That stamp is used for ANY extension of stay, including long-term ones, and generally means you need a re-entry permit if you want to keep your current permitted stay stamp "alive" when you make a trip to another country within the period.

A re-entry permit wouldn't give you any extra days than the current stay stamp (in your case, 5 Nov). And I don't think immigration officers would sell you a re-entry permit on a visa-exempt entry stamp.

You just leave Thailand by midnight on 5 Nov, then you will be fine.

Very good of you to read the stamp carefully and try to clear any uncertain points, which many people don't do often, then go into some trouble later.