Do tell us more abut your research.Actually, by my research, stones mentioned by Dunhuang Go Manual are not living stone on the board,they are captured stones.
But the Lanke Jing you refer to is a Ming document, almost 1,000 years later than the texts copied into the Dunhuang manual. The particular edition you show can't be earlier than 1508, I believe, as the only surviving original copy is preserved in Japan. The original was, I believe, written about a century before that but went through several editions.
We do know that a big chunk of it is just a copy of the Thirteen Chapters Classic (which was copied into virtually every book subsequent to C&IP, and the text you show is indeed from Chapter 13, as first given in the C&IP, and so relates to the same book that contains the earliest game records we are talking about here, where we already know they counted territory. The content of the C&IP can be dated to the Song period or a little before (but still well after Dunhuang). It is therefore a bit before Lanke Jing, but while the Lanke Jing is not telling us anything new, what it is indirectly and usefully telling us is that the same method of play (territory counting) was still in use in early Ming. The change back to stone scoring happened in the Ming but we don't know exactly when.
The Chapter 13 is entitled Miscellaneous and not really telling us anything about counting. It is rather a collection technical terms, proverb-type advice, tips on etiquette and notes on handicapping.
A key term in that text shown above is 路 (point of territory). Without checking, I'm reasonably sure this character appears nowhere in the Dunhuang manual. The key term there is always 子.