Do both itineraries contain the same flights?

The only minor caution I would mention here is that some folks buy tickets in certain fare classes that appear to be business, but are really an upgraded economy ticket. In the case of missed connections, the agents will sometimes rebook you into economy. I don't fly those tickets enough to know the nuances, but someone here can certainly provide more information on the fare classes.

If both itineraries are the same, then it doesn't matter - go with the lower price and enjoy the savings!