Yes, I did the EWR-ZFV connection, round trip, recently, with my family.

It seemed to work similar to a regular connection, with added complexity.

When you check in online for your travel, you do not get a train ticket. Instead you get a page that has confirmation number for train ticket. It instucts you to use an Amtrak ticket machine to get your ticket (by entering airline codeshare confirmation number). Unfotunately, the machine did not work (on either end) - this may have been because of multiple people traveling together in our case.

In any case, the ticket agents at both EWR and ZFV were able to generate the tickets very easily and without question. In fact, at the EWR train station, the Amtrak agent offered to move us to an earlier train since the connection was so long.

That move to an earlier train did, however, possibly cause complications, since the UA system registered us as having not taken the train leg and canceled our return ticket. I suppose this could also have been due to the conductor not reading the tickets properly or similar.

Luckily, I had checked the reservation in the middle of the trip and had it re-issued without problem, including same seats. This did require escalation to a supervisor. I did have used train tickets in hand and also had taken photos of our party on the train (done to generate time-stamped evidence of train travel) and would suggest you do the same.

The moral of the story is that UA does obviously track the train legs, no pun intended. They cannot be skipped. Of note, the train is much more comfortable that the plane.