Given the stages in the 3rd week, anything can still happen.
Someone could crash on a descent, someone else could loose time on a climb, someone could just suffer because of low temperatures or because of altitude.
I think that experience will play a key role in the 3rd week. Consider, for example, a stage like the Alba-Sestriere (20th stage). 5000 m of elevation gain, 200 km, 4 climbs, 2 climbs well above 2000 m, 19 days of fatigue already in the legs, low temperatures, long descents.
When they will reach the Agnello at 2744 m, the temperature will be just above freezing (and they will be lucky, usually at the end of October the temperature is well below freezing) so they need to plan carefully what to wear, when to slow down or stop to put on a jacket and/or other clothes, when to drink and eat something even if it's freezing. Moreover, the descent is 21 km long (2744 m to 1350 m) so they will be exposed to cold windchill for quite a long time.
Now consider that the same thing will happen on the Izoard, even though in less extreme conditions (the Izoard is 400 m lower than the Agnello). Then you have 2 more climbs to go, they are not particularly difficult but if you made some mistake on the Agnello or the Izoard you will pay the consequences.
If a GC rider blows out on the Agnello (kind of like Yates on the Finestre) he could loose at least 20 minutes. Same for Izoard (10 minutes) and Monginevro (5 minutes).