With the nomad prologue, you have to fix an engine. Other than that, there's absolutely no reason to open the front of back of a car. You can literally put a body in your trunk without opening it yourself. The animation will automatically open the trunk, drop the body and close it.
As for the stash in your car, you also don't need the trunk open for that.
So I'm sure it's a holdover from when there were going to be actual options and customizations with cars.