Thought I would update the forum with TfL’s response to me:
Thanks for your feedback of 19 March about interchanges displayed on our maps.
I’m sorry that we’ve not gotten back to you sooner regarding the points that you raised. I can certainly appreciate the perspective that all interchanges be favourable in terms of fare prices.
The close proximity of the services you mention are indeed useful, and we are of course always looking at ways of promoting the use of public transport. In recent years, fare structures have been used to do this. We introduced bus hopper fares, fare capping, and extension fares to make the structure fairer and more efficient.
When the geography of the railways in London is such that there is no realistic opportunity to make a given journey reasonably quickly without leaving one station and entering another en route, an out-of-station interchange will be considered as a potential solution. We do not have the authority to set all fares in London however. Out-of-station interchanges in the London area are determined through consultation with National Rail train operating companies.
We will continue to display information regarding the close proximity of different rail modes, but they may not all be set to being out-of-station interchanges.