does it matter as far as MoD are concerned?
Yes. Not least because the build standard / configuration of the aircraft is what the safety case is based on, and (presumably, but by no means certainly) MoD will have written a contract requiring one. So, for a start, a new version of the SC must be issued. If the changes noted above are correct, the MAA will (presumably, but by no means certainly!) want to review the decision.