Tuc,
There is no doubt that the MoD has pre-inquest sessions with the Coroner and without such cooperation things would grind to a halt. The Coroner needs access to official documents that may be classified, needs access to personnel and may need access to industry partners that operate within the MoD sphere of influence.
Does this offer an opportunity for MoD to influence things - undoubtedly. Have some in the MoD looked to exploit this - recent history records this as a fact. But the Coroner has primacy and is powerful enough to work through any MoD static. You are correct that the MoD did try to deny access to key witnesses in at least 1 inquest, but the Coroner just issued summons/arrest warrants. This did bring an unexpected reality-check to the Treasury Solicitors(!).
My point is that we have to trust the Coroner. If they use the powers they have correctly they will access the evidence they seek. There may be monsters out there, but they are not under every bed.