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I'd say you've been had!
If the vehicle was immobilized, and not destroyed, there is no way he can move through it.
In Cities of Death, scoring units are slightly different from normal games of 40k.
Strictly in cities of death, the only things that don’t count as scoring are independent characters and dedicated transports. So; for this case, the unit inside counts as a scoring unit as long as the unit is 25% or more. The transport itself cannot score.
I hope this clears things up a bit.