I haven't had any problems boarding at a later station, but I'm also not trying to board three hours later (the two stations I swap between are 15 minutes apart: CYN and RGH). I think you could talk your way on, but it might be stressful. If you rebook to change stations, Amtrak will treat it as though you'd canceled and then rebought your ticket at whatever the going rate at time of rebooking is.