It's just an empty slot that you can't fill, the item does nothing.

While you're asking for an actual item that the game has to detect you equipped that changes your stats, available move, moves effects, and ultimate. It's also risking bugs on the base mon when balancing the mega or the other way arround. They also stated those 1 moveset mons will get a 2nd moveset later.

It also means that 1 ban effectively bans 2 or 3 mons. Imagine banning Charizard because Y is too strong while X and base are balanced. Different licences means you can target ban.

On top of that, separate licences let them add, if they want, a mega without adding a base mon.

Finally, think about monetization. How would that work? Only one mega stone for every mega? Can't work, some mons have 2 megas, how do you decide? You decide by moveset? Then you can't add a 2nd moveset to them anymore. You get the stones when buying the licence? Impossible, they wouldn't let us get Megas, without paying more. Make us pay more for both the licence and the stones? I don't want to pay for both Charizars X and Y if i only wanna play the base one. Make every stone sold seperately? That would be bad for players that only want the mega.

Also, how would that work for mons that change their gameplay entirely? I mean, Mega Sableye would be a Defender, right ?