How they apply the metrics to arrive at a normal progression, or what metrics they apply is a mystery to me.
But to your other point, yes! If your employer had been getting prior approval for your salary changes by filing variances all along the way, then they would have nothing to complain about. That should be added in to the original advisory.
Apparently they are are also checking if the employer changed names, or was bought out, or if the address changed, but we have not seen refusals on these points. The refusals are only related to claimed salary versus work permit authorized salary.