Rebuilding Herne Hill station to accommodate that level of passenger flow would be fairly feasible, though, right? It wouldn’t require huge amounts of new track or anything.
I don't know whether it would be feasible - but as you're proposing this idea, perhaps you've looked at it? It's a constricted site, with buildings close to the viaduct on both sides at Zone 2 values. And the rebuilding would be disruptive while it lasted.
And I absolutely am accounting for passenger flows along the Chatham main line and the Catford loop! Increased service frequencies would make services more accessible, not less. And while the loss of connectivity to the current destinations is a cost, it’s made up for by the benefit of the connectivity to the new destination. Wouldn’t you say there’s an equal argument to be made about the current poor connectivity of the interchange at Herne Hill due to low service frequencies?
You keep going on about this extra connectivity. On what basis do you assert that this expensive project is necessary and desirable? Passengers on the Sutton loop already have single interchange access to Victoria, but somehow you believe that this isn't good enough - yet want to impose changes for those travelling to the City (from SW London) or Victoria (from SE London) when the existing services provide the basis for precisely those journeys. You also appear to want to remove stopping services from the Catford Loop to generate these notional benefits, yet I can't see where the impact features in your modelling.
For modelling purposes, its obviously worth considering how usage patterns would vary, and calculating those as (No. of passengers * change in journey time), allowing for the impact of changes in frequency. But that needs some real world thought. Each one of those numbers is a real human being, who has choices about their journey. They will place a value on convenience, which won't just measurable in journey time. Just as a trivial example, when I've used Thameslink from Wimbledon it's been because it's been hassle reducing to go one stop on the District Line to Wimbledon, then change there and pick up a coffee for a train that will take me to less than 5 minutes walk from the office. Put the extra change in, and I'm straight to the Tube.
If the capacity needs boosting (and I'm not arguing against that), then perhaps the answer is to bite the bullet and build a flying junction at Herne Hill - it couldn't be much more more expensive or disruptive than what you are proposing.