If you are building a custom pack to quickly set up multiple consoles, follow these steps to organize your .zip correctly.
Always back up your sysNAND via GodMode9 before running automated scripts from a zip file.
Ensure you have the latest boot.firm and boot.3dsx from the Luma3DS GitHub . These should sit at the root of your SD card (and thus the root of your zip).
Follow the on-screen prompts to "clean up" the SD card and install the system apps to your Home Menu.