Paint doesn't adhere well to grease pencil. The body was painted long before fire wall blackout was applied. Over time the paint flakes off and they become a bit more visible.
From John Z's First Gen Camaro Assembly Process article on the CRG site:
"The last process for a non-stripe car was the blackout booth, where the firewall was blacked-out, the trunk was sprayed with spatter paint, and sound-deadening undercoat material was sprayed in the rear wheelhouses. The rear "cocktail shakers" on convertibles were suspended in the trunk for spatter painting, but weren't bolted in place until later in the Trim Shop, after the taillights and marker lights were installed."
http://www.camaros.org/assemblyprocess.shtml