Those two LEDs are used to clip the signal when the switch is in LED clipping mode. So they can stay inside the box like on jovi’s build.
they will likely light up while you play (as they’re performing the clipping), especially if you have the gain set relatively high in LED mode. Some people like this feature in LED dirt boxes and drill holes and mount the LEDs so you can see them flicker. I probably wouldn’t personally do that on this build, since they’d only light up in LED mode, and wouldn’t do anything in the other modes.