sidey, I feel PD has got this the way I look at it, very often someone will spec something that is just not 'right', Ive often got 2.5mm radials spec'd with a 20 or 25A 60898 when there is no way that VD will be OK so I pop a 16A in, yes, its a variation, but its the compliant one, to do as spec would be a deviation that no one will sign for,
end point,
the contractor cannot legally with-hold your certs before payment, until you receive your certs the job is not yet finished, so you dont have to pay.
if the certs come back showing as installed , as opposed to as installed drawings , then you have a problem between your specifier and your installer, and you should seek some sort of clarification.