I disagree with your implicit understandings related to ko because these are not the only possible understandings.

The single black and white ko-stones are dead stones. This is why points "a" and "b" are dame (they are not surrounded by living stones of one player). The fact that a and b are dame was already discussed in the comments to Article 8. Points a and b being dame is why the 6 black stones (including the single black stone) are living seki stones. Yes, the single black ko-stone (黒一子) is deemed a dead stone when its life and death is assessed, but the 6 black stones (黒六子) including the one ko-stone are deemed alive when their life and death is assessed. 黒六子 have dame and so are seki stones. This is clear to me when reading it in Japanese. There is no discrepancy here. I don't know what rules you are reading.