Lets be quite clear it is on public record from the days when the OFT assessed the competion concerns of all bidders who pre-qualified that they have no problems with the same company running both franchises, primarily because they are in competition with air over the London to Scotland flows.
http://www.oft.gov.uk/OFTwork/mergers/decisions/2004/virgin#.Ut1vGX2nxcs
They did, however, rule there was competition concerns with the same company running both ICEC and XC franchises because of the overlap they would be the sole operator on 4 particular flows between Doncaster and Edinburgh with no prospect of competition from air or new rail entry.
That was 10 years ago. The criteria that OFT use to decide whether to refer to the Competition Commission has changed. The OFT can now apply their discretion not to refer to the CC where among other things that the turnover of the flows where there are competition concerns are less than £10m per annum.