What's new in GTK+ 3 dialogs

The example you give doesn't really have anything to do with the design ideal in question. The program could still have displayed a dialog saying "You have unsaved changes, what do you want to do? [Save] [Discard] [Cancel]" (and indeed many current editors do exactly this).

The problem with "Do you want to proceed? YES/NO" is that some applications used to ask "do you want to proceed?" [with quitting, i.e. don't save] and others asked "do you want to save?" with the same set of yes/no answers. If as a user I'm not paying attention or don't bother to read the message and blindly click, I might make a mistake and lose work. Why leave that hole open for users to fall into, when the solution is simple and need not be intrusive?