Weird, because when I checked, there was no icon indicating he could get a Mega Stone.
Guess later on, he'll get one but it'll be a different ability.
Until 1.3.3, Shiny Gyarados had a Mega Stone slot, but it shared the same stone from Regular Gyarados - with just one Mega Stone, you could M-evolve either Gyarados, Regular or Shiny (one at a time, obviously).
The same "rule" applied to other five variant Megas introduced since the 1.3 big update (Smiling Gengar, Costumed Sableye, Winking Audino, Shiny Rayquaza and Winking Glalie):
http://i.imgur.com/2REP136.png
The six variants, at that time, shared Mega-Abilities with their regular counterparts, and even the same amount of Mega-Speedups required. But I think these were only placeholders.
After the 1.3.3 patch, the Mega slot was removed from all six variants, so they can't mega-evolve anymore. But the Megas are still on the game code.
However: Audino, Gengar and Sableye Mega variants don't have proper Mega sprites yet, they reuse the Regular Mega sprites. So this needs to be updated too.