The only way to kill that mold is with chlorine bleach, or possibly Lysol spray. Since the carpeting has been removed, you can try spraying the sheet metal inside the trunk every day for about a week with Lysol spray.
If that doesn’t work, then you can try one of those pump-spray mildew products sold in the supermarket. Just be sure that you don’t spray this stuff on any wiring, seals, or gaskets. The painted sheet metal won’t like the chlorine bleach either, but on a 12 year old car, it is now an issue of your health or the appearance of the sheet metal in the trunk. I would opt for preserving your health, rather than the painted sheet metal, since inhaling spores from mold and mildew can be very bad for your health.