Yes, the JFK-Midtown one-seat ride has been feeding a lot of grist into the rumor mill. Nobody knows what form it will take as yet. As far as the LIRR's Rockaway Beach branch is concerned, the NY politicians have a paralyzing fear of NIMBYs, so instead of trains, you'll have burglars and homeless people on that ROW for years to come. (To my mind, it would be even today the perfect route for a LIRR express train from NY Penn or GCT to the JFK terminals, much like London's Heathrow Express from Paddington Station.)
I myself don't believe that PATH will serve the EWR terminals; however, the way it's worded in the report (it says, literally, "PATH extension to EWR" instead of "PATH extension to Airtrain Newark NEC Station") makes the language vague enough to make some people think that the PATH may indeed go into the airport grounds and possibly the terminals...