It's hard to visualize, but a ship's engine speed is only one factor in its overall speed across an ocean, even with powerful engines, wind and especially current will improve or degrade a ship's overall speed as measured by satellite. So a naive port fee based on time of departure will not exactly work.
It's a roughly accurate measure though. If there's a storm that slows them down, it would be perfectly acceptable for them to burn more fuel to arrive in port on time.
I think you are wrong about this, there are so many variables and sea conditions can affect things, for example older engines and maintenance at sea. AIS data is also known to be wildly inaccurate.
Source: built an engine performance model at a maritime company.
It's the ships speed relative to the water what causes any fuel consumption. For the purposes of saving fuel, if you don't know the water surface speed, you know nothing.
Precisely! You could be going slowly against the tide or current or weather and using loads more fuel - you ask anyone who has been at sea about weather and localised conditions that don't show up on satellites are common enough for me to believe the on ship reports.