Now that I understand the PDF better, and done some trial document evaluations with standardised text, I can see Agama's point about flexibility and reflow.
For anyone still reading this thread, I'll just say that PDF documents are the textual equivalent of taking a photograph of your document displayed on your monitor. You can still see all the relationships between objects displayed, but you can no longer move anything around, not even from one line to another.
Since I tend to re-edit and generate my own documents, I've never had an issue with reflow - it's always been there, even before WYSIWYG editing. And since most of my devices have a more-or-less equivalent display area and resolution, PDF was fine since it bypassed the limitations of minimum text sizes and so on.
But as an archive solution, I guess I'll keep looking. ePUB looks pretty good, in terms of definition and support (and I'm a huge fan of the Dublin Core metadata standard because of my work with audio recordings), but HTML rendering on the DX is abysmal, so for me it's a matter of an additional step to generate MOBI formatted copies of all my docs just for the Kindle.
At least now that I have better tools, I have more control over the amount and quality of text displayed, which makes my life a little easier.
Either way, I'm still using plain text as my touchstone "gold standard", since it retains the content, which is the most important aspect of archiving for me, since images and other gewgaws are irrelevant in the vast majority of book data I'm storing. Context I can figure out later, but as I said, EPUB is looking pretty good, with MOBI for the Kindle.
Thanks again to everyone who made suggestions and comments, and I hope this might be useful for anyone else reading this.
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