the Steelport in EtD is still the SR4 Steelport, they just added in the 3 Count Casino crib as a starting point
and it won't be possible for the ship to transport you to SR3 Steelport because the ship itself is hidden underneath the map, which is how it gets you into the city so quickly. When you "log in" to the simulation, the game just enables your outfit, superpowers, and weapons and teleports you to the area you select.
It might be possible to eventually replace chunks of the SR4 Steelport map with those from SR3, but not for a while.