As you are aware, the port of arrival in France, i.e., Dunkerque or Calais, must be indicated on your customs declaration when you exit Dover, which then restricts the driver from deviating from the specified port of arrival. However, this is no longer the case under certain circumstances, as detailed below:
Empty Units & Transit Declarations
If you are either empty or transporting goods only under a Transit declaration (full load or groupage under full transit), you may choose either Dunkerque or Calais at check-in without consequence. The potential change of the port of arrival will not cause your customs status to go orange. This means that you may check-in at Dover and ship to either Dunkerque or Calais, regardless of the destination port stated on your declaration.
Export to the UK
If you are transporting goods under any declaration, from France to UK, you may change the port of departure without consequence. This change will not cause your customs status to go orange. This means that you may check-in at Dunkerque or Calais and ship to Dover, regardless of the port of exit stated on your declaration.
Import to the EU
If you transport goods for import in to France, the port of arrival will not be updated on your customs declaration and the truck will be orange on arrival.
With the introduction of these customs formalities, if your vehicle is moving under a transit declaration, or is exporting from France to the UK, your driver can be more flexible with the route they take. For example, your driver may switch their port of exit from Calais to Dunkerque or vice versa at their convenience, thus having the possibility of an earlier departure and avoiding congestion.