[Quoth]

Kobo uses the NTrig/MPP type protocol. The cheaper MS surface 3 and later pens work. A Wacom EMR or earlier Wacom stylus will not work. An Apple Pencil will not work. A USI 2.0 pen will not work (I tried all of those). We know already they are selling the Kobo Pen 2 for the new Libra 2 Colour, which is the rechargeable version of the original Kobo Pen.

The markup will be like the 8″ Sage, except the Libra Colour is 7″. Unlike the Libra 2, it's 150 dpi rather than 300 dpi because it's the same idea as a mono LCD (all colour LCDs use mono panels), a filter adds colour thus resolution is less.

If it's basically like Sage software:
Only text markup from the epub done by keyboard can be easily exported.
PDFs are grouped only by the metadata at the time they are copied to the device. It's too small for PDFs (I have Libra 2 and Sage).
The Sage doesn't have layers, except PDF annotation is an extra layer that is visible if you copy the PDF back to the PC.
The Sage has two kinds of Notebooks. The sketch kind has predefined templates and the Advanced (with more recognition/conversion) has no templates, they use a cut down version of Nebo. The notebook system is completely separate.

I no longer use the notebooks or Pen on the Sage or Elipsa. I just read epubs and annotate them with the touch keyboard. I stopped using the elipsa except for some PDFs when I got the Sage.

There is no difference on annotation between bought and 3rd party content. I download Kobo ebooks to PC and transfer via Calibre, but I've tested direct bookstore sync like the Kindle has. I have Kindle too, and only use Download & Transfer from Amazon.

There may be 5 to 8 incompatible digitiser pen/stylus systems in use today. Some tablets can use two protocols. Most things only use one. Some 3rd party pens have more than one protocol mode, you pay extra. Also the NTrig/MPP pens used on the MS Surface can have an extra button that uses Bluetooth. That's not supported by Kobo. I've used the Kobo pen and two makes of 3rd party MS Surface (3 or later, the 1 & 2 used Wacom EMR!) pens on the Libra 2 (Sketch pad only), Sage and Elipsa (epubs, PDFs, basic notebooks and advanced Notebooks) and there was no difference, except the Sage is best.