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Well yeah, Sky clearly prepared Thomas to win the Tour in case Froome didn’t start. Not sure what to make of that.
deleted-
You're right; having actually read it fully, the headline is (predictably, I suppose) quite misleading.
Towards the end it says:
"Brailsford said: "We had two leaders - Chris was the actual leader,
Geraint the protected second leader - and the moment it dawned on him
that he wasn't going to win, Chris immediately switched to supporting
Geraint."
Harry 
SDB says the plan was for Thomas to win all along:
https://www.bbc.co.uk/sport/cycling/44997708