History... Back in 2011, there was a different balance of services planned, as shown in the London and SE RUS of that time. It had 6 tph via Elephant (of which none were from the Wimbledon loop), and 18 tph via London Bridge, of which 14 tph came up the Southern, and 4 tph off the Southeastern, but all via Tonbridge. So the latter would have come up through New Cross, and presumably not caused the same level of conflicts. But then by the time of the TSGN combined franchise announcement, (around late 2013 for Sep 2014 start), they basically announced that didn't work, and the intended future split at that time became the 8 tph/16 tph that I mentioned earlier, with no Southeastern trains via London Bridge, and Wimbledon loop trains re-introduced at 4 tph.
The key difference recently is putting Thameslink trains onto the Greenwich line. The infrastructure was always built to allow for the possibility of Thameslink <> Southeastern moves through New Cross.
As a bit of an aside, the alternatives report I linked to a few posts back explains that the Bermondsey diveunder actually started out as only a two track structure, and expansion initially to 3 tracks (for up Southeastern to Thameslink moves) and then later to 4 track (to include down Southern services from London Bridge) were decisions taken over 20 years ago. I also hadn’t realised that the very early plans had another flyover in the vicinity of New Cross Gate to get down Southern services over the Thameslink pair. I guess if that had been built it could have caused a major conflict with how the ELL eventually turned out.
