TfL doesn't actually run the TfL Rail services—the big difference is their operator receives a fixed sum for operating them, compared with the other operators where they pay a fixed amount to the DfT and pocket any profit they get beyond that. Arguably, the big difference is that it means TfL Rail will only get investment if TfL decides, because there's no motivation for the operator to do so. At the same time, TfL Rail isn't in competition with the Underground, etc. so better inter-modal connectivity becomes more worth investment.