This has a few implications:
Shown here is an overhead view of the beginning of Runway 31 at PAO. Notice that the markings in the area leading up to the runway threshold (the big white bar) are yellow, not white. Taxiways are marked in yellow, runways are marked in white. There are some other indications as well that distinguish a taxiway aligned with a runway from a displaced threshold -- see example, below.
Also, note the yellow lines on the edges of the taxiway that are perpendicular to the centerline, outside of the double yellow line taxiway edge markings. These are taxiway shoulder markings. Aircraft must avoid taxiing on the taxiway shoulder since it is not designed to hold an aircraft's weight.
This diagram shows an aligned taxiway preceding a displace threshold. Although this is not the same configuration used at Palo Alto (Palo Alto does not have the displaced threshold) it allows us to see a taxiway aligned with a runway and a displaced threshold in the same diagram so that we can easily see the differences between the two sets of markings.
On the departure end of runway 31 (the arrival end of runway 13) there is a 240' stopway (also known as an overrun area). This stopway is not allowed to be used for normal operation, but it is allowed to be used for decelerating the airplane during an aborted takeoff (aka a rejected takeoff). The stopway is added to the runway length for calculating the accelerate/stop distance available.