I'm not convinced they are though, even with dwell times slightly longer than say Farringdon, they still have eight an hour less than the TL core stations each way. In any case, even if CX trains used the TL lines through Borough Market they wouldn't need to use the TL platforms.
There are three tracks "reserved" for Charing X. The two nearest the southern lines would be the "fast" tracks and then the third would be effectively an up slow (in AM peak) with trains using platform 6 then crossing straight onto the TL lines through borough market and then onto the CX slows beyond borough market, staying unconflicting with the down and up charing cross fasts.
Similarly down trains in the evening peak from the Charing X slows would run onto the down TL at Borough Market and use either platform 3 or 4 before continuing along the down Thameslink or along one of the Cannon St lines enabing them to get to New Cross without any conflict with the Down Charing x fast.
Yes it is all conjecture, as we are talking many years hence but, the infrastructure will be there to do it and will be there for decades to come, and I think it will be too tempting a low hanging fruit to ignore.
Its certainly a very flexible layout though and a huge improvement on the '70s and '80s resignallings that took out a lot of capacity.
I'll try and explain one last time.
Morning peak - all trains off the 'slow' side of the SEML to CHX will be via Lewisham and down the Tanners Hill fly down, or on occasion, crossing on the flat at Parks Bridge. There won't be any trains on the slows London side of New Cross for CHX. There will also be 28 trains an hour coming out of Charing Cross, requiring full use of platforms 6 and 7 in the down direction. Even with a few ECS non stopping and squeezed through 7, it would be the height of bad planning to try and plan to run even one train 'contra flow' up through 6. It would take up at least 2, and probably 3 down paths. And then it has to slot perfectly in the middle of a 4 minute gap between up TL trains, and then 60 seconds later, perfectly into another 4 minute gap between the 14 down trains an hour on the Down Slow ex CHX that are heading to P6 and 7.
PM peak. The down train would have to fit perfectly into two exactly concurrent 4 minute gaps on both TL lines, and then somehow use Platform 3 which has 24tph heading the other way en route Cannon St to form the evening peak, or Platform 4 which could, maybe, squeeze up to find a spare path every 15 mins. (TL requires 90 sec dwell, 90 sec re occupation).
This project is spending a billion quid on flyovers, track and signalling to remove all these timetable constraints and prevent delays on TL contaminate SE and vice versa. It would be madness to unpick that core objective because it might be fun to play trains.