Why the printed number usually differs from the PDF page index
The position of a page in the file starts at one for the very first sheet, whatever that sheet is. The number printed on a page is whatever the document’s own convention says it should be. These agree only when a document begins numbering on its first physical page, which formal documents rarely do.
Take a report with a cover, an inside title page and a two-page contents section. Conventionally the body starts at page 1, and that body page is the fifth page in the file. If you stamp every page starting at 1, the cover gets a 1 and the body page that should read 1 reads 5 — every cross-reference in the document is then wrong by four.
The fix is the two settings working together. Restrict the stamped pages to 5 onward so the front matter is left unnumbered, and set the starting number to 1 so the first stamped page reads 1. The printed sequence then matches the document’s own convention, and a reader asked for page 20 finds the page marked 20.
If you want the front matter numbered too, the conventional treatment is Roman numerals on those pages and Arabic from the body onward. That is two runs: one over the front matter with the Roman format, one over the body with the starting number reset to 1.