Safety first.
Yes, you can use a real car trunk, but NO you should not shoot the interior of the trunk while the car is driving.
Does the rear seat of the car fold down? There's a perfect access for camera and sound. You can also shoot with the trunk open. Either way, you can use black flags, fabric, furni pads, or whatever you have to block light. Shoot in a garage so that you have a controlled environment (or a studio if you have access to one that can take a car).
Shoot exteriors of the car driving with nobody actually in the trunk, and if you need a shot of the trunk opening after the car is stopped, and someone in the trunk or climbing out, those are certainly just fine to shoot outside/on-location.