Waste is a line item, not a surprise
Make-ready and spoilage are different numbers, and both belong on the ticket.
Two kinds of waste
Make-ready is the sheets used to bring the press into colour and register. Running spoilage is the sheets lost during the run to misprints, hickeys and misfeeds. One is fixed per plate set; the other scales with the run.
Why the distinction matters
A long run does not reduce make-ready. It may reduce spoilage as a percentage, but the absolute number still has to come out of the paper order. Mixing both into one percentage hides the fixed cost and makes a short reprint look cheaper than it is.
The check to keep
Put make-ready sheets, running spoilage and finishing allowance on separate lines of the estimate. Deliver from the gross quantity after spoilage, and say so in the quote. If the client supplies paper, agree in writing who pays for make-ready.