The undercity during the Wrathgate quest is the same as the one you run around in normally. The only difference is that npc´s and objects are phased. The physical location of the zone and your character are the exact same ones as when you are in the ´normal´ Undercity.
So if they change anything in Undercity, you will most likely see this in the Wrathgate version as well since it´s the same place anyway. I say ´most likely´ because come Cataclysm, Blizzard is able to phase terrain as well, meaning that technically one phase could look entirely different from another, but that´s probably not how Blizzard intends to use it