It might have to do also with how much room there is in a harbor. A River Port like Philadelphia cannot accommodate ships jutting out into the river without blocking traffic. In the US there are probably safety issues in mind for firefighting and quick loading. A ship alongside a dock is easier to unload and fight fires with. Its also easier to allow crews to get on and off ships. In some European Ports the crews may not be allowed to disembark so parking them stern in doesn't allow them an easy disembarkation while still allowing the ship to offload.
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