UK military aircraft, including the Gazelle, were, historically, maintained to a Schedule peculiar to the UK military, and thus trying to transfer these aircraft to the civil register (other than on a Permit) is, at best, very difficult and prohibitively expensive.
The rational behind COMR (Contractor Owned, Military Registered) is that such aircraft are maintained according to EASA requirements, with monitoring contracts between MoD and the CAA. Thus the aircraft can be taken off the miltiary register and put back on the civil register with a full CofA. The benefit of this to MoD and the Contractor is that the through-life cost of the aircraft is lower, because at the end of the contract the aircraft will have a definable residual value: well above the comparable value had it only been maintained to the military spec.
BTW, the twist grip throttle on the (eg Australian and DHFS) AS350 was an official AS(EC) Mod, not a special military mod. A near identical assembly is used as standard on the EC120.