you should not make blanket statements like this. that's just fear mongering.
to summarize: as far as i can tell this pnr agreement covers flights to/from the us and flights through us airspace
Sorry but your references actually support what the OP said: the agreement covers all flights, not just flights from/to/over the US. The articles say that the agreement applies to airlines operating flights between any of the 27 EU countries and the US. Taken literally, this means it applies to all flights (including internal EU flights) operated by airlines that have flights from/to the US. I see nothing in the articles you mention that suggests a different meaning.