Fascinating stuff, ancient Vedic scripture has some vague refferences to advanced civilizations which existed.
I'm not a expert on the subject, but give the 3-4 billion year history of the Earth, it isn't a stretch of the imagination to consider the existence of pre-historic advanced cultures.
Humans are a funny lot as we are seeing right now with quite literaly a hysterical enthousiasm to erase history.
And as you mentioned why has modern science neglected to seriously investigate this Puma Punku site?
I be following ya!