Yep, that bothered me too. They are called stop words because, but only if, you filter them out. If you don't, they aren't stop words. There is no inherent "stop-ness" there.

I stopped reading after that. Some older NLP flows would eliminate stopwords, but I doubt any would eliminate "not". In any case, modern (i.e., last 5 years or so) LLMs don't