I find myself in some agreement with that statement. Ever since the DfT gave the TSGN reins to Govia using the mechanism of a management contract instead of a full franchise award, they have used GTR as a proxy to execute their more controversial intentions. Whether Govia could see how they would be used or not isn't (yet) apparent:
If they did, maybe they just decided that a fairly low risk 3% profit (or whatever it is) with the opportunity to blame the TL programme for any failures was better than the normal task of making a normal franchise successful.
Alternatively, they were naive enough to just accept the job, thought that they could make a reasonable fist of it, take the 3% and stand in good stead for future awards.
In the course of events, they were used to further Conservatibve party ambitions to take on the unions and force DOO on Southern services. The DfT didn't seem to get much blame for the strikes so that was a political win there.
Now, despite the DfT knowing the situation as regards GTR's failure to recruit sufficient drivers and Network Rail's delay in providing paths in time for training to progress etc., they (DfT) seem to have refused to accept that the project could be delayed. That would have politically damaged the government and maybe the current SoS in particular, (it could still).
Hadders' report from Monday's TSC meeting (post #2437) and later summary seems to be quite unambiguous in pointing a finger at the DfT, even suggesting that TOCs reticence to defend themselves against the civil servants might be seen as career limiting. Such is the farce of the 'privatised railway'.
Since the 20th of May, the DfT has not been seen as the cause of any TL problems, the mainstream media choosing to place the blame on the TOC and/or NR because they are organisations that the travelling public have knowledge of. I have felt that they in some ways are the stakeholders, the funders and effectively in control of the major decisions to go with the changes and feel that they will be rumbled sometime although they will probably try to take TOCs and NR (who they control anyway) with them. As Hadders says, maybe the TSC report will include them as a major part in the failure of the changes so far.