If I recall correctly, I think the system still provides a little bit of a grace period between the stop you purchase and the stop you board at.

I thought it was around a 2 hour window.

When Amtrak first started Eticketing, there was no grace period and there were many angry customers that were upset when their reservation was canceled when they boarded 1-2 stops down the line.

This may no longer be the case, but, back before AGR 2.0, I would routinely purchase a BOS to NYP ticket and get on in Providence, RI (PVD) to get the 500 or 750 points for a Select City Pair.

My reservation was still in the system at PVD and easily scanned by the conductor.