Yea, you don't want to automate this. You need to keep your resume personal and truly tailored to the job. Unless you really work on natural language parsing the job description and the "about" pages of the company website, it's going to be a lot easier to do those little modifications yourself.
And as you said, you want to make sure the overall narrative flow as well as the overall design of the document makes sense for the job.
And as you said, you want to make sure the overall narrative flow as well as the overall design of the document makes sense for the job.