Anybody fill the area between the trunk / fenders?

High end vehicles haxe foam in those sort of areas to serve as sound deadening and insulation. They have the foam fill and a plastic bag and shaped so it can be removed and put back again. This is likely what your body man has in mind.
It's my belief that all the nasty found in that area came from a failed trunk lid seal above rather than up from the road. What gets in around a quarter glass should stay in front of the wheel well.