Even if the GW did what some are saying they did, who cares? They are making all the work, as long as it's safe to use the exploit and their launcher on the original GW card, they could even make the launcher draw dicks on screen when used in other carts. Also, we are fucking pirates. All of us. Even if you only use it for something else, I've got news for you: You're a pirate. We all are using (or about to use) something that shouldn't be used in the 3DS, so, anyone who purchases and use one of this carts are consciously aware of the risks. Our machines can get bricked. Also, I don't care, if the cloners copied pretty much everything GW did, in our country we have a say that literally translates to "a robber who robs a robber, has 1000 years of pardon", but, if they have that right, why shouldn't the GW team have the right to code some traps on the launcher? As long as it's safe to their consumer base, they can do whatever they want with it. "muahh, but they are bricking peoples machines", NO they are not, the USERS are bricking their own machine, because they know there's always the risk, even more if they know they are purchasing a clone cart. If they don't know it, they shouldn't even be purchasing a flashcart.
People shouldn't also be using custom versions of the launcher because they covet some feature. If they want that feature so bad, ask for it, the developers have showed so far that they want to give what the users are asking for. Just be patient, and they'll add it when they can. Modifying the launcher is always risky, and people should be aware of that, so, to take precautions, they shouldn't even be shared freely.
TL: DR: Because, reasons!