My 2015 MKZ Hybrid trunk lid does not pinch the rubber molding very hard, nor does it get close to the metal body. Sounds like there may be a need for an adjusting. According to my service tech, Lincoln sends along a gauge with each car for the dealer to check ALL body panel alignment upon arrival off of the transport. Nothing should get close enough for metal to metal contact.
I would reach out to Lincoln Client Relationship Center again even with photos to show the chip in the paint as well as the torn rubber molding.