I took John's advice and spoke with the owner of the company. According to the owner, at the time that I met with the salesperson, the company did not quote the price for full flashing replacements so that the bid would be competitive with other roofers who do the same. He said that now he requires his salespeople to include full flashing in the estimation to be more transparent. He was not happy that his project manager reached out to me about the additional charge for full flashing replacement the night before the job was to be started.
My original estimate includes "install[ing] aluminum counter flashing to all masonry chimneys." You'll note from the image that I attached with my initial question that the additional $2,300 for the recommended option of full flashing replacements includes installing heavy duty step flashing at all side wall applications and at all head wall applications. It also includes installing new flashing tapes if no house wrap exists and installing new J-channel siding.
This will bring the total cost to replace the 25-year-old roof and adding a seamless gutters system on our 2,800 SF two-story house to $14,789. This is the cost estimated before the roofers begin the job and potentially uncover additional issues.
I am planning to pay the additional charge because it sounds as if not doing so could subject our home to leaking in the areas that would not have full flashing replacement. However, if you have anyone available to look over the information above to let me know if s/he thinks full flashing is important and if I am getting a fair deal, I would appreciate it.