I don’t think it would help to retain full pdf formatting.
Tinderbox isn’t a tool for storing things: we have excellent everything buckets in DEVONthink, Yojimbo, Eagle Filer, and indeed Finder. Tinderbox is an analytical tool, and it works best with short, focused notes.
Tinderbox extracts the main text of the pdf in the expectation that you’re probably going to split it up and organize it. But there’s no point in spending hundreds of thousands of dollars to recreate formatting which Tinderbox won’t be able to reason about — especially since you can link the document to any Tinderbox note and have the actual document displayed with a single click.
The most common pdf import discrepancy is that Tinderbox will grab what it considers the main text, and might ignore a sidebar that you want or a long footnote that you need. Just grab those with copy and paste.