Honestly, I don't know what it would look like, but being able to query would be deeply important. But what I can say is that a lot of the PDFs I work with are auto-generated as PDF forms using queries, after the information was likely inserted into a relational database during some esoteric transcription step.
Meaning, the information that formed the PDFs very likely come from a relational database and an inversion back to its original relational form is probably the convenient form. Whether that means it turns to 40 tables, that's fine, so long as it's relational and a query can be written.