@Marti-MG I hope I'm not too late.
If you want to use GPIO18 (PWM_CH0) only then you should remove U6 the 6 pin SOT23 marking C145 SMD IC only.
See also the official Omega-Power-Dock schematic.
After this modification Power Dock 1 remains fully functioning. You can check the battery level visually with the pover-dock command as before - but the 'battery level check' scripts will not work of course. Power Dock Checking the Battery Level
You could probably use the Omega GPIO's through open collector transistors or mosfets to drive the LEDS, then you won't have to worry about the 5V supply as it is isolated from the Omega's 3.3V. Read up on which GPIO pins to use though as some have special functions and you need to disable them using the omega2-ctrl gpiomux command