I think it's hard to blame Ineos. Crans Montana did have the headwins, and Thomas did push to the line in that stage and it's not like Roglic was close to dropping there.It's funny how these kind of things go. All of a sudden one really has to ask why he didn't attack Roglic in the 2nd week. Who knows, Ineos might have thrown this Giro away by not applying any sort of pressure in Crans Montana.
Maybe you can blame them for not putting Arensman or De Plus in a breakaway, but that's once again similar to the Jumbo 2020 scenario. When riders are in the lead or virtual lead, they generally won't use team tactics to put a teammate in GC.
In hindsight you can say they should have gone harder on Bondone, but I don't think Thomas ever had the surplus of strength needed to make a big move that he didn't.
The equation with TGH in the picture would of course have been way different.