The following is true for the Chevrolet world and I'm pretty sure it's true for Pontiac too.
In 69, all body #'s were the order confirmation #'s. That is, the confirmation # assigned to an order when it was placed was then used as the body #. Obviously cars were built in a different sequence than the orders were placed.
VIN's and build dates are the only things that you can compare between cars.

So, why would some orders sit? Supply issues and line balance issues. Most often, the shortage of a component (anything from an AC seal to an engine model) would cause the order to sit. The scheduler would put the order in the build queue when the components were all in-house.