In most repair shops, the hourly rate is jacked up to cover this as an overhead cost, just like insurance, rent, etc. Since the advent of computers, it's become a method to itemize such supplies, and add it automatically. Just because you can categorize it now, it becomes a charge.
I can't imagine adding nails, screws, saw blades, drill bits when I was building homes years ago, nor a fee for 'forms' and stamps when I sent an invoice. That stuff was all in my cost projections.
It's like buying tires - we get a 'quote', then when the invoice arrives, a tire disposal fee, a shop fee, state tax, fed tax, town road fee all adds to the 'original out-the-door' charge. I always look at the OTD price once I arrive, and if so, THEN compare it to the size of the check I will write, not the phone quote. Sometimes, it makes it worth leaving and buy the tires elsewhere.
OTD quote should be dollars we write on the check amount lines.