The VIN is the chassis not the engineIf a ferry company found the discrepancy you mention I cannot see that they would have the rights to act as you suggest. They would have to call the police.
The ferry company could presumably refuse boarding to that vehicle to avoid a sailing delay.
If they got it wrong in checking, e.g. because the vehicle had had and engine change so the VIN on the block was different then they could incur liability.
I think the ferry companies would consider the hassle not worth the disruption to loading plus the extra staff costs.