I began roofing when I was still in high school. Summer job that paid for my first truck. When I would tear off, especially three tab, I would rip off layers and go back to get the nails later. Having vents, pipes, etc just took more time. This is where the additional “remove” cost comes in. Take a straight gable roof with no accessories and a straight gable roof with 10 accessories. Which will take you more time? Of course you can justify this, if you are being fair and reasonable.