Ben, again, thank you for sharing your thoughts and conundrums. Rarely do people take time to develop arguments nowadays.

I often forget that a 'professor' in America is a colloquial sobriquet that a high-school teacher may adopt in addition to academic rank at universities. I would be honoured if it were the latter.
I shall guess at my "three words" might also appear in the next sentence. Don't conflate tacit Weltanshauungen!. Note, I didn't call you out over you using "Zettelkasten".

Until you choose to extract your notes into "full documents" that stand on their own then your Zettelkasten collection is your entire corpus.
Each Obsidian note can be a micro-collection of your images, vectors and prose. The key point is such a grouping has all the back-links accessible and you have an automatic visual graph of all of these to interact with.
This diverse dataset can be collated and distributed as a standalone entity. The end-user's "reader" is simply Obsidian, free to all.
If unavailable, the note can be exported as PDF or HTML.
In contrast, Affinity can produce an integrated PDF but all associations and interconnectivity now has to be hand-crafted. Users can search the PDF but not readily across a clutch of them. Few will have access to Affinity so your source is locked away, binary-encoded.

Producing a "website" of PDFs is a non-starter. PDF viewers are not standardised and rarely accommodate display sizes. I use a Kindle and reading a PDF book is dire at best.
Do read https://www.thesitewizard.com/webdes...e-in-pdf.shtml

In Windows, indexing of PDFs is usually done with an installed Adobe PDF IFilter for full-text searching. Needed as the PDFs are binary-encoded.
In Obsidian, you are full-text searching on plain text. The search results of both are sentence fragments but Obsidian's is across your entire Vault (corpus).
Timing is therefore immaterial.

If you have a closed community like Apple, Adobe and Microsoft, even Serif & Xara, you will always be at their mercy.
Open formats like XML, JSON and Markdown transcend the bearer systems.
If it were my legacy, I would be after something that will be preserved for decades. Paper is still the best medium with and for plain printed text.

Acorn