The people who did the calcs did it based on a freshly caught Mewtwo. Since we know Mewtwo's stats they could work out it's IVs and being just caught it would have no EVs. Then Mega evolve it and calculate MegaTwo Ys stats from Mewtwo's base. I believe so anyway
Well, I know that. However, I didn't see the images that reports the stats of mewtwo's normal form. And I heard from so-called spoilers that the mewtwo's nature is lonely, that is +Atk-Def.
Also, I know from the demo version that the physical defense of mega mewtwo Y didn't decrease so much (from the damage from Lv.100 Dragonite's attack)
Therefore, I would like to believe that mega mewtwo Y's nature is lonely.
From the video of demo version, we can find that Dragonite's water tail hits the mega mewtwo Y (68 HP). According to our calculation, a dragonite(Lv.100, Atk:IV0 EV0: 273) using water tail should damage mewtwo (Lv.100: IV31, EV0: 216) at least 82 HP, which can be represented by the following equation:
82 = [(0.4*100+2)*90*273/216/50+2]*0.85
Even if the Mewtwo is +Def, Dragonite is -Atk, which is the extreme case, the damage can not be 68 unless the random number (217~255) is less than 220. So, if mega mewtwo Y's def base is 70, the damage can't be 68 unless the mewtwo has EVs.
The demo video can be found on the youtube.
The video is found:
In this video, Dragonite's water tail damages mega mewtwo Y 68 HP.