I took delivery of a 2017 MKZ and have observed some of the same issues with what appears to be rattles or popping noises from the headliner area and around the rear doors. I worked in the high end audio automotive business years back and was paid good money to alleviate rattles.
From what I see it's actually the trim on the outside of the doors along with the rubber seals where the doors meet the body. You made mention that it usually occurs on cooler days when the plastics/rubber is not as flexible.
Go to your local auto parts store and purchase silicone lubricant preferably grease and place a small amount on the rubber seals everywhere you can on the doors, trim, etc..
This will help with the contact between plastics, and rubber along with rubber touching metals. If you look closely you will find that the car has this type of lubricant on many of
the rubber gaskets from the factory.