I just rebooked a September SFO-EWR for a 5 minute change and was able to get SFO-IAH-EWR for about an extra 500 miles. Because availability was wide open, I only moved up from N to G. If you wait until closer to departure date, you might be able to do better, but only if there's nothing lower available.

Also, in my case, ITA said the cheapest available was Q, and yet they booked me into G.
Similarly, United.com well let me have the SFO-IAH in L, and the IAH-EWR in Q (so together I have to book Q).
So I think they can stick you in a fare that they wouldn't otherwise sell.

For me, I'm just going to keep adding a connection every time they change something