The goal of the QMK software project is to develop a completely customizable, powerful, and enjoyable firmware experience for any project - keyboard or otherwise - and to provide helpful, encouraging, and kind support and feedback for people with any software development experience.
Only try to read the report ID from SetReport when the keyboard is part of the shared EP
If the keyboard has media keys or NKRO on, SHARED_EP_ENABLE is automatically enabled to merge them into a single endpoint (see #3951). The different interfaces are then identified by a unique report ID. However, the keyboard interface is by default not part of that shared endpoint unless KEYBOARD_SHARED_EP = yes in your rules.mk, and so it does not need a report ID.
The end result is that when LUFA tries to ask the host which LEDs to turn on, it expects there to be a report ID byte first, then the LED state. It will then set the report ID to the actual LED state, and no LEDs come on.