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Thomas was the perfect candidate to be the protected rider with the Froome case hanging over the team. If Froome was prevented from starting the Tour, then Thomas would have happily led Sky. With Froome starting, Thomas' lack of ego meant he was happy to accept the second leader role and, probably, happy to ride for Froome if required.
I think what few expected was that Thomas was the strongest rider in the race.
You're right; having actually read it fully, the headline is (predictably, I suppose) quite misleading.
Towards the end it says: