The whole project is a financial boondoggle, it is designed to benefit the properties which Flagler Development owns in downtown Miami, Ft. Lauderdale and West Palm Beach. As for the expanded shipping in and out of Miami, it probably will never happen because of geographic factors. Miami is in the wrong place and it is too far from manufacturers or other major markets. No one is going to ship their goods for hundreds of extra miles by costly rail when they can do it a lot cheaper by going through Ports to the North and in the Gulf. These are factors no one in Florida can control.
As for the super mega container ships coming into Miami to unload and pickup goods to transport to the Far East, that even makes less sense. The only Port which currently can handle large container ships is Norfolk, Virginia which already has better infrastructure than Miami can ever build and it is having trouble servicing the extra container traffic from one large ship.
The large ships will stop at transhipment facilities in the Caribbean (there are some existing and a few more being built) and the transhipment facilities will service all of the Ports on the East and Gulf Coasts by smaller ships. Maersk and its competitors have already recognized that they will have to use transhipment facilities if they want to keep their Mega ships full and moving.