As promised,..

My flight was the 8:30 pm EWR-BOS, of which I had booked a connecting Amtrak segment from ZFV (Philly amtrak station) to EWR. My check-in time for CO was approximately 6:51 which is after my train "arrived".. and it was successful at the e-ticket machine at Penn Station. Haven't checked mileage posting but I'm sure it will be fine.

Thanks nyc_flying_gal and everyone else that contributed their experiences! Hope it lasts.