On this News article, in the third paragraph,
“by the time it taxied to a halt, it had one more passenger than it had started with”
Does that mean, the baby had been already born before the airplane started to land at Narita airport?
Thank you in advance. 
You got it exactly right.
“The plane was given priority to land at Narita Airport, just outside the Japanese capital, but by the time it taxied to a halt, it had one more passenger than it had started with.”
Even though the plane got a fast landing (priority), it was too late. The baby had already been born before the landing. “it had one more passenger than it started with” is just the writer trying to be cute or witty rather than writing the sentence in a clearer manner.
So, this “one more passenger” means the new born baby, then? Thank you, xophist!
Yes, you are right. Well done.