The MATZ system was set up in the mid-1960s when few aircraft were fitted with transponders and overall air traffic density was considerably less than today's. The intention was to offer a degree of additional protection to military traffic operating in the vicinity of bases but without adding the complexity of legal obligations.
The main differences now are that most aircraft are transponder-equipped, airspace restrictions are considerably more numerous and air traffic in certain regions (such as SE England) is greatly increased.
If a military aircraft was carrying out an instrument approach in IMC, what protection would it have if an intruder decided to transit the MATZ without negotiating penetration clearance? Suppose the intruder was not transmitting Mode C, thereby rendering TCAS (if fitted) ineffective, with no TAs or RAs. Perhaps the intruder's radar return (mode A or primary for non-transponding aircraft) would be picked up by the MATZ controller but what could he or she do apart from vectoring the aircraft carrying out the instrument approach around the intruder, which might mean breaking off the approach.
Perhaps there is a case for MATZs to become mandatory 'listening zones' (VHF or transponder) to allow transit without ATC exchange. Think how much quieter the R/T traffic would be.