Sure but once it has been broken it can be included in the application by default or am I missing something like that it's different every time? The program might as well use the encryption of publicly released ROMs then.
We can't write a completely self-contained ROM decryption tool on a computer because you would need:
1. The normal-key for keyslot 0x24 of the 3DS.
2. The algorithm used by the hardware key-scrambler.
An operation (number 2) is performed with number 1 and the key you can generate with the keygen that's part of the CTR_Decryptor toolset to produce the title key used to decrypt a game. We need 1 and 2.