Right, of course, but here the first "flight" is not a flight, and I think Jackal has it right when he says Amtrak does not / cannot report individual boardings in anything close to real time. Amtrak has a scan-to-check in system -- you print out a bar code / PNR, take it to a kiosk, and print off your boarding tickets there. But not a scan-to-board system. So I think in the short term Amtrak can tell whether you've checked in for a trip, but not whether you actually rode the train.

The OP might try checking in for his train trip via kiosk at Penn Station, then heading out to EWR. I do not know if Amtrak's system can tell that you checked in at a kiosk far away from your intended boarding point.