The new CF650 systems may be able to operate quite happily alongside S40 with a bit of geat sat inbetween them, and indeed do interoperate on Neasden Depot, so it could be the case of some running to Harrow OTH and some met still running on the local lines (possibly the Uxbridges) off peak there shouldn't be a need to use both fast and local lines for the met.
It would proberbly result in a system using three northbound and two southbound platforms at Wembley Park.
And yes, there are very significant issues in using centre sidings north of the stations to terminate, the only realistic place on route that you can terminate Jubilee services early without significant operational issues is North Grenwich...(!)
Might mean an additional turnback North of Harrow OTH towards Moor Park though since the Harrow OTH Local Turnback would be pretty much exclusively used by the Jubilee Line.
Oh, and if it's done properly one could be looking at service something like
(If we include facilities to use different N/B platforms at Wembley Park)
Peak
12tph Harrow OTH - Stratford
12tph Stanmore - Stratford
6tph Wembley Park - North Greenwich / Stratford (Stepping back at N Greenwich)
Willesden Green and West Hampstead would no longer be used for turnbacks under this plan, but it would proberbly need a significant amount of stock to pull this timetable off.
A bit more work; removing the unused fast platforms at Willesden Green and/or taking up some extra land at West Hampstead to provide three jubilee line platforms with a similar layout to Golders Green or North Acton to be used for turnbacks (Works very nicely on the Central Line). This would reduce the amount of trains required and remove the need of south facing junctions for the Jubilee at Wembley Park and reduce queing Met units that will share the entry with the Jubilee onto the Harrow OTH Locals, so for both stock and timetabling this would be optimal.
West Hampstead looks a bit tight, but it looks acheivable at Willesden Green, possibly by sending the N/B Met 'round the back' of the Met platform, that becoming the Jubilee Northbound, terminating on the current Jubilee Northbound, additional space in the siding if required or going back south again (same island), install stepping back and you're all sorted to terminate up to 12tph (technially up to 17tph) at Willesden Green. If neither of these can be done in the peaks everything will need to be pushed through to Stanmore or Harrow OTH.
So that would be 18tph to Stanmore and 12tph to Harrow OTH. One would not like on reflection to be using centre line terminating anywhere other than dedicated or semi dedicated platforms. (Such as the layout at Seven Sisters)