Are you sure about this?
Not long ago Zerodha was still charging, but didn't call it penalty but charged 2x brokerage. It was a spread position, exited long leg first and end up with margin shortfall for few seconds. For that they charged 2x brokerage. When asked they said if any orders got executed while the available margin is in negative, they would charge 2x brokerage. If they didn't call it penalty back then, probably they are still doing it. Don't know how it is today with Zerodha. Anyone who actively trade with Zerodha can tell.