Just as Flow's win looks even more impressive when you look at the films it competed against, who produced them, and what resources they had, Blender has been a project competing for parity and to be taken seriously while remaining totally free, and going up against systems that are either wildly expensive or not available outside the studio that made it at all.
Flow is not good because it was made with Blender, but Blender is proven to be very good and in that top echelon because Flow was made with it. For those who make or use Blender, this is big. Those folks have already believed for years/decades that Blender was great and serious, but now a lot more people outside that circle will know this, too.