This is a real issue that is often glossed over. Obviously you can't have wires under the 'cranes' so you then end up with separate site shunting locomotives with all of the (un)coupling, brake tests, stabling point and so forth. These cost money (up front and ongoing), waste time, reduce terminal capacity and increase safety/performance risks.
Bi-mode locomotives with 'last mile' off-wire capability can help here but are themselves more expensive, require more training, are possibly slower when off the wire, etc.
For very short freight branches (possibly including London Gateway but also Tilbury2, Seaforth, East Midlands Gateway, Birch Coppice and so on in due course) it may well not be worth the trouble of designing and managing a wiring 'project' when there are other more straightforward routes to be done.