Having listened to the ATC recording, it is clear that the controller descended the flight to height 600m on QFE, but the readback from the crew was 900m on QNH corrected by the controller to 600m, the crew then requested confirmation of the QNH which was given correctly by the controller, but if the the crew were using QNH instead of QFE, it was not picked up by either the crew or the controller, this, if I interpreted the RT calls correctly would lead to a descent to roughly 300' below the cleared height.
To me, this would suggest a high level of workload, either before the confusion in setting the altimeter, or resulting in possible confusion in verifying the correct altimeter setting and correcting the error.
Whether or not this had any bearing on the outcome is speculative, but it may have been one of the factors combining to produce the top event leading to the loss of control.