How do I get rid of this rust in the trunk?

If you don't have the option of blasting the metal to get down into the pits, VHT makes a great rust converter.

Wash the area with a good de-greaser or warm soapy water - dry it off - spray on the rust converter nice and thick - wait a few hours - make sure all the rust has turned a dark black - wash with warm soapy water again and then re-apply some Por15 and forget about it.