So, I have been thinking about what the 2018 Tour looks like for Nibali, assuming he rides it. If Froome is the rider to beat, which seems reasonable enough, then the head-to-head in this year's Vuelta would be a place to start in terms of assessing what is likely to happen.
Nibali lost about 1:20 between the TTT and the ITT, over a combined 50K or so, about :20 over 13K in TTT, and about 1:00 over 40K in ITT. So, over a little more than 30K in the TTT, he seems on track to lose 1:00, and over 30K in ITT, about :45. So he is down 1:45 on that. Assume Froome continues to beat Nibali on murito finishes, so he loses time on the stages to Mur de Bretagne and Mende. Say that adds up to :45, or, being pessimistic, 1:00. That means he has 2:45 to get back on the rest of the stages.
If Nibali is in form that approximates his 2014 performance in the Tour, then the first place to look for him to get time back on Froome is the cobbled stage. I don't think it is reasonable to expect the conditions that prevailed in 2014 to replicate themselves, and Froome did not even make it to the cobbles, so no basis of comparison on that day is available anyway. In 2015 Froome did not have any problems with the cobbles, but that was a much smaller amount of cobbles. So assuming Nibali actually does have an advantage on cobbles, perhaps 1:00 would be what he could hope to gain. The stage to Quimper might offer some options for Nibali, as he did well on the stage to Sheffield, but that gained him two seconds, plus bonuses if they apply. So we are up to a minute and ten seconds in a fairly best case scenario.
That leaves a minute and a half he needs to pick up on the rest of the stages, which effectively means the mountains. In the last week of the Vuelta, setting aside the time Nibali lost on Angliru as a function of his crash on the previous descent, Nibali picked up forty seconds on Los Machucos, but gave back twenty seconds the next day. So there is some precedent for Nibali gaining time on Froome in the last week of a GT (see also the last week of the 2015 Tour, setting aside the Alpe d'Huez stage, as Nibali lost a chain at the worst possible time.) but that is about twenty second there, so he still needs a minute and ten seconds.
Froome beat Uran by only :50 in the 2017 Tour, but it did not really seem that close. I don't see Nibali beating Froome in the 2018 Tour. Not unless Nibali has 2014 form, and the 2014 form was actually good enough to beat Froome at the time. Nothing in Nibali's recent GT results suggests that is likely to happen, as he has been unable to beat Dumoulin, Quintana, and Froome in his last two GTs. But, if somehow he does manage it, and does it purely on the basis of superior form, then Nibali answers a lot of questions about how strong a GT rider he is. I admit I am hoping he can do it, as it would also put to rest the minimization of his previous Tour win. It just seems like a lot to hope for.