The 5v reference is supplied through a regulator, then a resistor.
The PCM (or whatever module) is supplied source voltage, or battery voltage. It then steps down that voltage though a resistor and feeds that reference voltage to whatever sensors need it. So if the 5v reference is shorted to ground, it's after the resistor internal to the PCM.
Think of it like a light bulb with a voltage supply and no ground. You'd measure voltage on both sides of the bulb. When you supply ground, the bulb drops the source voltage. Now think of the bulb as being internal to the PCM. You wouldn't be able to measure voltage in, but the wire coming out of the pcm would have 12v, until you ground it. Then the bulb would be the load and drop the voltage instead of blowing a fuse or burning a wire. Only instead of bulb in the PCM, it's a resistor.
I hope that makes sense.
