Can confirm it works fine online, at quik trak machine, and with agent for single trips. Amtrak is one of the approved suppliers so it will function like any other debit card. Whether or not your trip meets the definition of a commute is a different matter but the card will work.

ETA: Read the original post and question again. I had a similar situation and used WageWorks fine. My departure times were set so I was able to book my trips far enough out that I got the discount bucket fares. This and the number of days I had to be on site meant it was cheaper than getting a monthly for me. The downside was you lose the convenience of having choice of trains when your schedule does change. You end up needing to track credits/refunds more diligently and redeeming points at the last minute. WageWorks works fine for this and definitely not tax fraud if it's still your commute.