You might consider using a product like Evaporust. It would sit down in the trunk grooves, or you could soak a rag in it and lay the rag over the surface. With a little time, that should get the rust gone. Then you could clear over it to keep it from rusting, or scuff and repaint inside the trunk.

Evaporust shouldn't harm your body plugs or seam sealer. It might help on the trunk mat too.

Tav