I believe you may have answered your own question. 'Use Customer Specification' and 'Use Document Specification' are separate print jobs, because potentially every document could have a different specification. 'Use Document Specification' is a new option, but 'Use Customer Specification' has been around for a while.

If you want to have a single print job and a single file created, you need to pick the 'Use Selected Specification' choice, guaranteeing that only one spec will be used.