Where XYZ comes from
The point-cloud form has no author and no specification; it is simply what surveying and scanning tools produce when asked for coordinates, and it predates any of the formats that tried to standardise it. The chemical form comes from the computational-chemistry world, popularised by the XMol program in the early 1990s, and is the default input of nearly every molecular tool. The two grew up independently and collided over an extension.