Didn't the Stelvio neutralization on/off query also hang on the context of "what is an attack?" in that several riders stopped for rain gear and some continued through the summit? i.e. Quintana, Hesjedal and Rolland did not leave their group per se, they just continued to ride, whereas those that stopped voluntarily left their group out the back of it?
Ultimately, what was ok and what was not was not clarified by the race directors, and some people played to the whistle and got an advantage they perhaps shouldn't have had, and others stood around like a defender sticking their hand up waiting for an offside flag that should come but doesn't and were stuck with a disadvantage they shouldn't have had.
In my eyes, this one's on the race organisers for botching the handling of it, badly, creating a situation where nobody can be happy with the end product. Taking an arbitrary amount of time away from Quintana is meaningless and artificial (after all, where did the faux-neutralization end, and what was the time gap then?), but leaving it as it is disadvantages Urán who can justifiably feel wronged. However because the organizers were not clear enough, Quintana hasn't been adjudged to have broken any rules, hence they can't eject him. So we're left with sticking with the results that were prejudiced by the organizers' poor handling of the matter, or introducing a highly artificial additional variable to attempt to right that error which produces a result which only has tangential relation to what happened on the road.
Basically, Quintana keeps the race, Quintana has one of those dubious GT wins that forever goes in the annals of time, like Moser's Giro with the helicopter or The Stolen Vuelta, but if they penalize Quintana and Urán takes it, the GT win comes with the same dubiousness, because he only would have won due to an artificial and arbitrary time penalty applied by the organizers to cover up their own error.