Indeed, that's the logic that's led to the Rainham and Maidstone E. services being routed this way. But has anyone really quizzed NR/GTR on why Windmill Jnc. can't handle it? It's obviously a busy junction, of course, but this constraint was never raised in the public inquiry when powers for Thamesink project were obtained. The ELL has added some trains to WCR and more or less hard wired them into a 15 min cycle, so is this weird plan really just a long term consequence of both adding trains and having them run clock face (not really SR practice in the peaks, so as to maximise capacity...) And how essential is it that the TL operate at 24tph instead 20tph? The current TL implementation plan worked out by Chris Gibb's group has the Rainhams being introduced last of all. My guess is that actually means 'many years hence': although the Bermondsey Flyunder and LBG rebuild permit a very sensible sorting out of the approach tracks as has been pointed out on here, it's obviously somewhat messed up by introducing this crossing move into the Greenwich line. It might make more sense if the Rainham service (if it ever does run) was plumbed into the Bexleyheath route and back via the Angerstein link to Charlton...but that would probably (finally) make the flat crossings at Lewisham inoperable (at least in the up direction). Or if more CX to Greenwich line trains (if they ever come back) were dropped and the TL trains could be dropped precisely into those slots timing wise.
I think GTR are being overambitious about 24tph, for one thing, and especially for the Southern end of there are alot of branches linking not only four important main lines: The Brighton, South Eastern, Midland and East Coast main lines along with several major South London suburban lines such as: The Catford line, the North Kent line and the Sutton loop.
Crossrail only links the Great Western and Great Eastern main lines along with interchanging with the North Kent line at Abbey Wood and is relatively self contained as a route,
I think at the moment rather than adding extra routes and slowing down journeys on other lines (ie: The North Kent) GTR should run 20tph and once Windmill Junction is ironed then Thameslink can roll out 24tph along the Sussex routes as originally intended in a few years time, especially since South Central terminal platforms have been reduced now and will inevitably clog up platform space,
That way Stopping suburban Sydenham trains can run through the core as planned.