score:9
From page 105 of Network Rail's Sectional Appendix you can see a map of the station. From East to West there are five lines:
Trains to London from Southend can come around the double track line that you identified and directly join the mainline to London, or join the London slow line by just crossing 1 line (Mainline from London).
In contrast, a train from London on the slow line (the majority of services) is on the "wrong" side of the station, and would have to cross three lines to get to the Southend Branch, so instead uses the flyunder. Trains using the mainline from London either cross one line onto the slow line away from London and use the flyunder, or cross the mainline to London and use the double track section towards Southend.
The flyover appears to be on 1930s OS maps so is rather older than I might have expected.