I shudder when people use page numbers for referencing, and then require fixed-format documents to support this. As you say, the page numbers don't always translate across "documents"... sometimes even if the output format is ostensibly the same.
Two different versions of the same document renderer are capable of producing different page contents. Two similar fonts with the same weight and point size (but slightly different metrics) are capable of producing different page contents.
You end up getting in arguments over which is the "true" document.