The loss of attack doesn't matter much, except for one EXTREMELY crucial thing. Without a +atk nature, Mega Rayquaza cannot guaranteed OHKO Mewtwo Mega X from full with Dragon Ascent:
252 Atk Rayquaza-Mega Dragon Ascent vs. 252 HP / 252 Def Mewtwo-Mega-X: 396-468 (95.1 - 112.5%) -- 68.8% chance...