I agree with @Starlet_GT that the engine was changed so registration had to be changed for the engine. So only that change is reflected in the book.
Since the Chasis still contains engine number plate of the original engine, ofcourse it will not match with the new engine number on the book or on the engine itself. No issues on that regard.
But the point is that the car is not Japan assembled anymore now, is it? A major modification was made on it locally. In that context you will have to assess whether the price is according to the market rates or not.