I have the same question as the OP. After having to experience automatic rebooking twice in the past month (sigh), it seems that there is no perfect solution and you are better off just going to customer service.

Yesterday I went from SEA-SFO-SAN. I had UDUs clear on both segments. The SEA-SFO was late due to ATC so I missed my SFO-SAN flight. I got automatically rebooked on an evening SFO-SAN flight in F, however there was another flight 4.5 hours earlier with availability in coach (but not in F) that I did not get rebooked on. Since I would rather get to my destination 4.5 hours earlier I went to customer service and got rebooked on the earlier SFO-SAN flight. SFO-SAN is such a short flight, I am a little surprised UA's automatic system would assume I would want to wait an additional 4.5 hours just to sit in F.

A few weeks ago I did SAN-DEN-BOS and had used a confirmed regional upgrade to get the F seat. The SAN-DEN flight had mechanical problems and I would have missed my DEN-BOS connection. UA's automatic rerouting would have gotten me into BOS 6 hours behind schedule and in the middle of the night (ouch) - also in Y because presumably no F seats were available. Went to customer service and told them I want to get to BOS asap, and they got me a U.S. Air ticket instead. Although it was all in coach, I got to BOS with only a 2 hour total delay - much better than arriving in the middle of the night.