I think we have a different opinion on what constitutes a "Fakémon". To me, the definition is "a Pokémon that was created for the hack that does not exist in the original game". I've been asking some questions in the quick questions thread, as I see most hacks use Fakémon with my definition. Keep in mind that when using Krookodile and its earlier forms, they're all Fakémon; they are not part of G/S/C or R/S/E.
Now, if the original idea of a game is to redo the Pokédex, that's one thing. I've seen Pikachu in one listing video way up in the 100s instead of his standard 25. In such cases, the redo of the Pokédex makes sense as it's a regional Pokédex; even Unova's gets a makeover with the new Pokémon that are considered part of the Unova region. The National Dex, however, I'm sure still lists everything the way we're used to with their original numbering. These hacks basically forbid use of a "National" Dex; since only 386 are programmed into the game, and Krookodile is #553, using a National Dex would replace someone else with it in the listing. This is where the Fakémon bit becomes obvious: in the post-E4. Where later generations are programmed in like this, the National Dex cannot exist at all. I'd be worried about a trade between games if someone did burn this to a cart. themselves and put it in a system; someone could be collecting an unknown Pokémon in another game (Rattata anyone? LMAO).