I'd only figure it in if it was an unusual situation. Normally cleanup, paperwork, all the other shop stuff not work directly on the job would be overhead and should be part of the shop rate. If a particular job required something unusual and I anticipated that, I'd figure some shop time to do it.
OTOH, if you're just a lone operator and are deciding how to quote a job it's perfectly fine to say, "Well, it will take 4-1/2 hours to machine, 20 minutes to sweep up, 30 minutes round trip to the UPS office and another 15 minutes to pick up the fasteners required. I'd like to make at least $15/hour for my time so that, lets see, 5 hours, 35 minutes @ 15/hr so I'll quote $83.75 for the job." The customer doesn't need to know how you arrived at that. He either accepts the price or argues with you, or goes somewhere else.
"In theory there’s no difference between theory and practice. In practice there’s a lot of difference.” Yogi Berra