I also use the 3% rule for each run. I now run sample sheets for lining up different color runs that help cut down on 3%, but there are always the few that go in crooked. So I am happy to have the 3% overage.
I generally print 25% extra, to both account for spoilage and to have samples for the designer and for myself. I know that’s a lot, but it lowers the stress level!
I created a spreadsheet with at least 10 parent sizes so I can calculate how many out of a number of standard sizes all at once. If the 25% causes a new sheet to be used for only a few press sheets, I won’t cut that one. I can also choose a different parent sheet size to minimize price and maximize how many out of a sheet.