So I ended up touching down at EWR at 2:10 yesterday, with the EWR - ZFV Amtrak codeshare not assigned until 6:30 or so. My girlfriend and I both had poor flight experiences from SEA and were not going to wait that long (The gentlemen in 27C took all of her 27B legroom, and I had some enormous baby carrier wedged in the seat behind me).

Anyways, we were exasperated to the point I was fine paying for the next train. I spoke to the 3:05 Keystone conductor that rolled in, explained that my tickets weren't for another 3.5 hours and asked if I could hop onboard. He told me to call Amtrak customer service once I was onboard and request a change (train was fairly empty). Once we got going, the customer service rep told me that she successfully made the change on her end and that the conductor would see the adjustment when he scanned my ticket. I can't confirm if that was the case, but regardless I was at 30th St by 4:15 and on my couch by 5:00 without any additional fees.