Eh!! my first comment up here! 1. When you optimize on an ice type, for example, Mewtwo automatically appears, however if you go to the list of pokemon, there are two mewtwo icons to choose. 2. Yes it does, it changes. 3.Since there are two mewtwo icons they are two separated megas :( you need to drag the candies to the Mega X one. 4. Yes, it appears. 5. Two mewtwo icons.
https://www.reddit.com/r/PokemonShuffle/comments/4636kl/anyone_got_mega_mewtwo_x/d02458w
So, looks like its two icons - one for each