It's SUPPOSED to be that you can transfer airlines, as long as your ticket is an equal or better fare type (eg, you can't use a ZED low when your agreement is ZED medium) and equal or better zone (that EWR-ORD ZED won't take you to HNL instead, but you can use it to get to BUF if that helps you out). But again, taxes vary from one airport to the next, so origin can't be changed.

Of course, that all depends on the agent's knowledge. Plus, with etickets things get a little weird anyway.