I know this post is old, but it is still useful to get an answer.
Changing the layout could be:
Physically, the props still spin in the same direction. but the motor numbers are changed: for example, when using the omnibus flight controller with 4-in-1 ESC (designed for Betaflight), one has to set the parameter MOT_ORDERING to Betaflight/Cleanflight. Note that if you need a different motor ordering, it is totally possible, but requires some a few changes in the firmware.
Change from CCW to CW and vice-versa : the only axis affected is YAW. Therefore, you just need to change the sign of the yaw gain in the mixer fileR: 4x 10000 10000 10000 0 -> R: 4x 10000 10000 -10000 0
Hi. I think this problem is actual (e.g. if some motor pwm out was burned), so it’s better to answer late than never.
I found array with output definitions in a platform-specified code (e.g. for fmu-v4), where pwm states are written: