[Quoth]

There is no problem with Kobo Annotation. I've 4 Kobo ereaders.
Kindle is rubbish in comparison. I've used PW2, DXG and PW3 for annotations.
Proofed 100s of books. I use the Kobo Utilities on Calibre, but you can add a menu item per book to export a text file just for that book. It has the highlighted text, chapter if exists, % through book, and note entered.

You can't sensibly use the Stylus on Sage or Elipsa for real annotation as it only has the handwriting to text in Advanced Notebooks. You use the onscreen touch keyboard to enter notes, though a BT Keyboard sort of works on any Kobo with BT (doesn't stay connected).

Kmate does nothing that Calibre Annotations does for Kindle, won't run on Linux and inferior to Kobo export or Kobo Utilities on Calibre. I tried it on Windows.