I never said anything about a unit that works on 4th rail as well as OHLE, not sure where you're getting that from. My argument is bonding the 4th rail means you can use standard 3rd rail trains (or more relevantly, standard dual voltage trains). It is my understanding (and please, correct me if I'm wrong), that all TfL's 4th rail trains work fine on bonded 3rd rail, so the S-stock should just work (let alone the fact it already does so at Wimbledon). Unless you bond the 4th rail to make it compatible with 3rd rail units, you're stuck with using diesel trains until the whole shebang gets OHLE. I guess bi-modes could solve that issue, but still.
The benefit of the temporary state of bonded rail means you can commit to the project in smaller chunks with minimal disruption. You can incrementally bond the rails with zero changes to services, and both the existing Met stock and the future Chiltern stock can use it. Installing the OHLE between Aylesbury and Amersham has no impact to the diesel services, so that's fine. Chiltern stays as diesel, the Met operates as now to Amersham, abet on increasingly bonded 4th rail.
Once you've finished the bonding between Amersham and Harrow and the OHLE between Aylesbury and Amersham, you can then introduce the new dual voltage rolling stock for Chiltern and cut the Met service back. You then convert southwards from Amersham to Harrow at leisure.
I do agree with you, it probably would be cheaper to rip up the 4th rail and install OHLE all in one go, but you'd have to withdraw the Met service and somehow find diesel rolling stock to provide the service between Amersham and Harrow whilst you did the whole project. I think that approach is too risky, you may disagree.