But is the actual measured gas flow the same as the stated gas flow for a particular set of specified conditions.
Unless the boiler output has been set low for some reason, there's no reason why it wouldn't be. And it's easy enough to check, just read the meter over a timed minute, or longer for higher accuracy.
But even if gas flow is low, it's that which might be causing the low hot water performance, not boiler efficiency being below spec.
Do those specified conditions include the temperature and humidity of the incoming air for combustion.
As I said in earlier post, I assume testing would be under specified conditions - flowrate, temperature rise, flow temperature etc, to give comparable figures between manufacturers, but I don't know full details. Maybe incoming air temperature, but I doubt whether normal variation of RH would cause a measurable difference. I don't think it was ever explained how somebody claimed 126%, but that's been beaten to death.
Does the tally include the rise in temperature and volume of combustion air passing though the boiler ?
It's irrelevant. If the heat into the water, and the heat in the gas are determined, dividing one by the other gives efficiency. For a given boiler on test, the rise in temperature and volume of combustion air are what they are.
Boiler efficiency figures seem to be the efficiency of combustion and not the overall efficiency of getting the heat produced by combustion into the water.
I still don't think it's possible, or necessary, to split boiler efficiency into combustion and transfer efficiency. Dividing out by in gives overall efficiency.