Jon, what you say could be true of decisions relating to London transport infrastructure, but is not true of timetables relating to Southern and Southeastern, whose services extend beyond London. TfL has no say in those. DfT produces the 'specification' that sets out which services Southern and Southeastern is required to operate.

And, see the latter part of post #450 for clear examples of DfT leading and influencing TfL in decisions relating to transport in London.