Many customers assume that this score refers to the number of pages on the site scanned as compared to the total number of pages on the site. This is actually incorrect!
The score is essentially a "grade". It is calculated using a complex formula that looks at the total number of passed tests for all pages divided by the total number of tests performed. This is weighted as well so that errors represent more than warnings and notices.
We do not provide the exact code used to calculate that score, and due to the complex nature of the calculation, it's unlikely that customers would ever be able to reproduce the exact calculation on their own.