Sky were able to play other teams' cards, rather than their own. Froome attacks (or follows attack) Dumoulin has to chase...Thomas just needs to sit on his wheel.
What you have to remember is that without Dumoulin's mechanical and subsequent time penalty for drafting team cars. Thomas's advantage would have been a mere 32 seconds.
Whilst Thomas got everything right, he also had no bad luck whatsoever. This was a really close race, a fact that will not be lost on Sky. I think Froome will do Dauphiné + Tour combo next year, possibly with Thomas as plan B. There is no way that Sky will base a Tour team solely around Thomas, all other things being equal. Sky might not even contest the Giro next year, at least not with their A team.
As for everything else , in many respects Sky were very lucky that things panned out the way they did. Froome is, and always has been, utterly toxic, and despite ESL's flights of pure fantasy it has nothing to do with which school Froome attended. A Froome win would have actually dented Sky's reputation even further. As it stands he got the chance to reinvent himself as selfless, self-deprecating and loyal team-mate, which in all fairness he probably is considering that he is also a ferocious and determined competitor.
Sky have jumped the shark.
