How much can the 5v ref be off?

I was playing around looking at my knock sensor, and one thing I did was to unplug it completely and check the ref voltage. I saw that at KOEO it was only getting about 4.59v. Battery voltage was about 12.59.

How much can the 5v ref be off from 5v before it represents an actual problem?

I think what you are looking at is a bias voltage rather than a reference voltage.
Reference voltage is a tightly controlled supply voltage that provides current flow through sensors such as pressure sensors and tps sensors. A bias voltage can there for two reasons:
1 To allow the PCM to perform a circuit integrity test -- to flag up if the wiring is broken or sensor disconnected.
2 Lift an AC sensor output above the zero volts line so it becomes a DC signal more suitable for the engine computer to deal with.

In the case of a Knock sensor it is a piezo device which would normally produce a AC signal so by applying +4.59 volts bias the signal becomes 0.1 to 9.2 volts dc.

But why such a weird number? I would expect it to be a bit more round...

The ecu isn't really looking at maximum and minimum voltages it will be similar to how it reads oxygen sensors it will be looking at crossing counts ie how many times the signal passes through threshold voltages in a given time frame.

One ting to keep in mind is that when measuring very high impedance (ie high resistance ) sensors like piezo knock sensors or the circuits that connect to them just measuring the voltage can alter the the voltage yo see. ISTR Paul ran into this problem fault finding a speed sensor circuit with a Voltage Probe type tool. The voltage probe had a fairly low input resistance (istr around 4,000 ohms) which was enough to put so much load on the circuit it pulled the voltage down to close to zero. Normally a decent multimeter has an input resistance of around 10 million ohms, and scopes are a standard 1 million ohms.

Which video is that from Andy? I'd like to take a look at it.