I'm imagining PDF as an "XML file analog", to be mapped into the W3C's ecosystem.
... Expressing in another words, is Adobe's PDF signature thingy in any way compatible with general-purpose file-signing tools specified at [XML DSIG Core]?
As @SteffenUllrich suggested, a "real-world use case" will be fine... But this question is about simplifications and abstractions, so the better is to (only) imagine a use case.
Use case: a published article of a government gazette. The article is a digital document with legislation content. The publsisher house must to publish in two formats, PDF and EPUB (or other XML-based format), both with the same signers, and they using the same tools and same certificates.
The technical staff of the publisher house must to answer the present question, to ensure to auditors (as well as citizens, lawyers, etc.) that both signatures (XML and PDF) will use the same tools and will have the same level of reliabilty.
The "analogy map" is also to move from the "strange Adobe-centric universe" to the W3C's ecosystem view.
Of couurce, each format have different fingerprints (different checksums)... Imagine the PDF and EPUB as products of the same matrix (the content must be the same), they are like "twin sons" that will use same infrastructure whenever possible, reducing production costs and audit costs.
... In the real-world the "twin sons" like XHTML and PDF are producs from a XML matrix, by XSLT and Prince convertions, and, after convertion adding a commom workflow to use digital certification (signatures).