What's happening when the shared Met/Chiltern parts are re-signalled? I would expect they'd take the easier route of retaining tripcocks or substituting TPWS but in either case operated by the new equipment, rather than the potential nightmare of fitting a Metro TBTC to a DMU most of which are 15+ years old. Although the same solution would probably be used between High Street and Junction for the Overground service, there would be no need to fit the section in between unless some sort of through service like this one was envisaged.
I have absolutely no idea yet.
But you are correct in that a moving block signalling system such as CF650 or TBTC (S40) is not very simple to combine and/or integrate onto any non-homogenized stock. This includes Chiltern Stock, but also the 66s on RHTTs on the Met Fasts, A60 RAT, Battery Locomotives, Engineering Vehicles and other alien train moments.
And in
my opinion, this needs to be very seriously considered when any new system is installed or overlayed.
I do have some very reasonable ideas that could be integrated into the design without very much hassle at all, with a few overlay / handover points on the network locked with a form of fixed block SSI and then handing in/out to a moving block system (if installed) using wayside limits of authority (as are already used on points and crossings). This would handle any handover points with Network Rail track (Watford High St Junction, Great Missenden, Neasden, Gunnersbury and a few other potential points), while allowing a high core tph, without unessesarry upgrades in other areas.