Can I assign a taxonomy to a content type's term_reference field at runtime?
You can create a Content Type named Vehicle and make inherits his fields to your Cars, Van with the help of the Bundle Inherit module. Then you can create a Taxonomy for each kind of Vehicle then you will have.

Vehicle (color, number_of_seats, etc)
 - Car (field_car_tags)
 - Van (field_van_tags)


With this you don't need to write lines of code and you can reuse the fields of the Vehicle Content Type.