According to the official Pokemon X and Y site, PokeTransfer has a filter that detects when a Pokemon that has been illegally obtained and disallows it from being transferred. However, whether of not your Pokedit Pokemon will get past the filter depends on many things, like how good the filter is and what it checks.
So it may or it may let you or it may not. Seeing as Pokedit is one of the most popular methods of illegally obtaining Pokemon, the filter is likely to have some way of finding if it came from a website like Pokedit. However, since the app if still unreleased, we don't know. We'll have to wait to find out.
>Note: You may find yourself unable to use Pokémon Bank or Poké Transporter to deposit any Pokémon created illegally by software unauthorized by The Pokémon Company and Nintendo into your online Boxes, or to move these Pokémon between online Boxes. ~ http://www.pokemonxy.com/en-us/strategy/