I agree there's a mismatch between the Agile Manifesto and most of the concrete methods described as "Agile", especially when it comes to how much individuality is valued. I am not at all convinced it's fair to blame this entirely on the methodology side. The eXtreme Programming book was published in 1999 (and had been talked about before then). Scrum is a little harder to pin down, but a book was published in 2001 (around the same time as the Agile Manifesto), but the ideas were definitely circulating before that. There were other concrete methodologies which fed in, _e.g._ Alistair Cockburn's "Crystal" methods, which seem to have faded away.

In any case, the people pushing the methodologies overlap very substantially with the people who originally signed the manifesto.