You are missing indenting. That's very important in the config files. This ought to work:
Edit: I noticed just after posting that the homing definition also had RGBW. I removed the W setting as it's no needed (your color order only has GRB, not GRBW).
Code:
[neopixel bottom_leds]
pin: PB6
chain_count: 42
color_order: GRB
initial_RED: 0.0
initial_GREEN: 0.0
initial_BLUE: 0.0
[led_effect homing_probe]
autostart: true
frame_rate: 24
leds:
neopixel: bottom_leds
endstops: x, y, z, probe
layers:
homing 2.5 0 add (0.3, 0.3, 0.4)
Edit: I noticed just after posting that the homing definition also had RGBW. I removed the W setting as it's no needed (your color order only has GRB, not GRBW).