1)"The article read that he had stayed in NY except for the weekend at Greg's during which he started to paint, and that they met on board the Queen Elizabeth when they were coming back from Europe."
Are they correct? Would there be a difference in meaning between these sentences? Can we say "the article reads"?
Articles normally say or state rather than read.
I am a minimal comma-user, and would have one only where I have inserted it in #1.
As for the question I have underlined, I will leave it to others to try to satisfy your apparently insatiable determination to find absolute rules for each and every conceivable use of the past perfect.