Yeah, the Zeners are not functioning once the circuit is running - they exist only to protect things until the regulator kicks in, around 20-30 seconds after startup. So the actual Zener voltage depend on the miniscule leakage currents of the individual diodes, e.g. on how much fingerprint was left on the diode.
The only time it is important is the initial check, page 36 of the upgrade manual. Here the initial voltage of 345v is set by the Zeners, and the eventual voltage of 300v indicates the shunt regulator has taken over. After that, if the regulated voltage is right and you can adjust the driver plate voltage to the correct value, then you can ignore all the readings on that terminal strip.