This aircraft did NOT stop within the available runway, which ends either at the end of the threshold or the displaced part. It stopped within the over-run area (or stopway) which is not considered part of the runway.
To see the difference look at figure 2-3-6 here:
Section 3
There is an important distinction in that one part of the runway is used in landing calculations and the other isn't.
This crew was lucky - had they been somewhere like Chicago Midway and travelling a few knots faster the outcome could have been a lot different.