I'm banking on this idea too, unless they intentionally designed it to look similar to Satoshi's clothes, it's important to remember that the magazine said it resembles his clothes. XY's main feature? Customization. I'm guessing the future starters in Z will take on similar appearances to their trainers via Customization, Mega Customization in a sense. Which also allows them to receive a power boost and maybe a stat change? It's also important to note that it's called, "Satoshi Gekkouga" so unless that naming will be a universal thing in the game, (unlikely I thinnnk) then that means the Pokemon will take on names of their trainer like we see with the Mega Evolution naming template. I'm not sure if they would design a Mega to look intentionally like Satoshi, he may have received his clothes for that sake and advertisement sake but the other way around would be odd. I think Mega Customizable Kalos Big Three will be a reality in Z, with something about bonds, which also allows Gekkouga's change to be not super duper forced since Satoshi and it barely have a bond to begin with and it would explain the absence of a Keystone, it also has its rivalry with Shota and Juptile.
Worst case scenario, some type of anime-exclusive Mary Sue feature, which would really suck. Though I wouldn't be too upset if that was the case, if only because this new form Gekkouga looks absolutely terrible while regular base Gekkouga looked great.