[Quoth]

If you want to control even your ordinary ereader functions and have sensible local USB control of Collections, series, covers and annotations, forget a Kindle that's not jailbroken, and many versions can't be.

Only the reMarkable seems to be a poorer thought out eink with pen based note taking.

The Kobo Sage and Elipsa have four methods working by USB for Notebooks:
1) Copy the actual Nebo files to something else with Nebo
2) Exports as images in standard files.
3) Conversion to text and export a plain text file
4) Mixed content of converted text, converted shapes, converted maths and handwritten or freehand drawn as docx.

No WiFi ever needed. The Scribe has no writing, shape or maths conversion. Kobo sensibly bought in a package with good rep on iOS and Android. It uses Nebo.

Actual PDFs on Kobo seem to be annotated with an extra image layer, just copy the PDF back.

The epubs are best annotated with text. I've not investigated how drawn/handwritten annotation of epubs is exported as I've no interest.

I was seriously considering a Scribe for PDF proofing as it's 300 dpi vs 227 dpi, but it seems you can't use it without Amazon except as a reader only.

So I'll wait and buy a 300dpi version of the Elipsa, for now my 8″ Kobo Sage seems better than the Scribe to read ebooks and make/write notebooks. It's not bad for PDFs too now that the crop setting is remembered. So though I got the Elipsa first, I only use it for PDFs and freehand annotation of them. The Sage is a better size for writing or reading epubs.