Contractors do not charge for paperwork directly. That point would be moot.
When I spec'd a home with a builder I demanded plywood subflooring and stated I would pay the cost. He told me some outrageous figure that was about twice what I would pay for just the plywood without any rebates or compensation for the OSB board not used.
I agreed to pay it and then was told,
"We don't build that way, anyway. Go elsewhere, is you want that". I did.
As Lew stated, this is where the contractors make their money...not on competitive specs. Hurts, but when you do it, you will too.
So, how long?