I understand your concern, but I don't think edited distro roms would be a very large problem. There are not many people around who would go on ebay and search for a gen 3 distro cart without at least some knowledge of save editing and roms. The large bulk of people who play gen 3 these days also do so with emulators, which would lend itself to this. Even for people who do play legitimately, most people who are interested enough in pokemon/gen iii to know about distro carts, let alone buy one, have searched pokemon enough to know what can be done and be aware of the free option.
In other words, to be successfully tricked by a fake distro, someone would have to:
1) Be seriously interested in gen iii
2) Be unaware about roms/emulation
3) Have the necessary hardware to actually use one (which is pretty rare these days for people who fulfill both of the conditions before this)
4) Actually have and be willing to invest the prohibitive large sum of money needed to buy the fake
Because of that, I seriously doubt people would get tricked by bootleg distros.
Also, I'm not even sure that those bootlegs would even pop up on sites like ebay. We've had custom DS distros for years and I've yet to hear of a bootleg DS distro, even though bootleg DS games have been a problem. Maybe they might pop up on Aliexpress (I honestly doubt even this, but it's possible) but the people who go on Aliexpress tend not to be those who would fall for the fake distros. If I were a bootlegger, I'd much rather sell bootleg games in bulk than try to get lucky with one distro hack.
Even then, it is totally possible to actually put in a failsafe for people to not fall for the fakes. You could make a closed-source editor with a start screen similar to Pokemon CrystalDust's, which bootleggers would not really be willing to brave.
But this last point aside, I honestly feel like actually putting forward anything found would be a major service to the community. At least for me, making custom distributions is one of my favorite aspects of Gen IV. I have lots of fun memories of handing them out to friends and classmates, and it honestly lends itself to a really good time. Sure, you could just trade them the .pk3, but part of a mystery gift is the actual experience of giving out the gift, which is lost with a simple trade.
All of this said, I still understand the concern, and I obviously have no influence over what any dev does. I would like to ask, however, that if the modifications aren't made available there should at least be a 10 ANIV Celebi distributor, because Celebi is the only Pokemon for which an English language version can't be obtained like Nintendo intended (which is kind of funny, considering Celebi is the only Pokemon missing from the Mystry Mew saves' Pokedexes). I think that's something we would all like to see.