How do a comprehensive eye exam and a routine eye exam differ?

Less detailed. In many practices a routine eye exam will be a brief exam that does not include a detailed exam of all of the parts of the eye. In addition there is typically no discussion of any medical issues associated with the eye.
Perhaps nothing. Most times a routine eye exam actually is a comprehensive exam. While you may not have anything wrong with your eyes, when you go in for a routine exam, the exam itself will be comprehensive in scope. That is, the front and back of each eye, the eyelids, and surrounding tissues are examined. A sensory exam is also performed, including vision, pupil reaction, motility/vergence, and visual fields.