I didn't say that tracks 1-4 didn't extend past 8th Avenue. I said:
Only the platforms for tracks 1 through 4 do not extend under 8th Avenue.
And yes, Farley sit on top of all tracks that serve Penn. In fact Farely even sits on top of the small yard that NJT uses for feed some of the tracks at Penn that you see to your left as you leave Penn and head for the tunnels.
The A Yard, the C Yard and the Diagonal Platform all sit under Farley. There has been some talk of converting the Diagonal platform into a usable passenger platform too. The ladder tracks to tracks 1-4 pass under Farley. According to plans, Farley will be connected to tracks 1-4 using pedestrian walkways suspended above the ladder tracks and the yards too.
Of course with NJT now out of the picture for Farley, there is really little need to connect those 2 platforms to Farely since it's rare that Amtrak would ever use one of those dead end tracks.