This pretty much matches with my experience of trying to do what I had posted earlier in the thread.

I basically wanted to give myself more than 4 hours connection time in EWR so I could spend the day at the office. I could not find a phone agent who was willing to adjust just my BOS-EWR segment, leaving my EWR-PHX segment untouched.

Each one said I would have to pay $150 + fare difference because I was trying to spend longer in EWR than the fare rules would allow.

However, I had no problems getting on the 6a flight from BOS-EWR at the airport.

Furthermore, once I flew the BOS-EWR flight, then the website would let me adjust my EWR-PHX flight online to my heart's content. This ultimately allowed me to push back my EWR-PHX flight to the next afternoon which was the ideal for me, schedule-wise.^

If anyone has advice on how to get the phone agents to do what the airport agent had no problems doing, I'd really appreciate it.

But my lesson learned here is that it looks like you'll have to get the airport to do what you want to the first segment, but then you can do the rest online like normal once that is flown.

As an aside, having this waived, and the ability to do all of this online even after you've checked in is a huge perk from my perspective, and one that I would value greatly if AA would do as well. The online aspect combined with the +/- 24h window made adjusting my plans incredibly easy and removed a ton of the maneuvering that I ordinarily would have had to do if this were on AA.