Testing a reference voltage of a ECU
Is there any other way of going about this?


Yes - to simulate the "condition of absent of reference voltage", simply cut the PCB track (or equivalent change) to disconnect the output of the voltage regulator supplying the reference voltage, from the rest of the circuit.

But

Total loss of the reference voltage (as you described) is only one of many possible failure modes of the reference voltage. If you only test for complete loss of the reference voltage, then you are only simulating a limited percentage of possible faults that could occur with the reference voltage.

I am not a specialist test engineer, but I can easily think of several more possible failure modes of the reference voltage, which could (and, imho, should) be tested for sane behaviour, with something as important as an ECU.