Check Airman,
I don’t know what FedExs’s manuals state and this is not a comment on their actions. This is my opinion.
My outfit doesn’t prohibit fly bys but does strongly discourage them. I agree. The tower operator isn’t a pilot (most likely) isn’t an A and P (most likely) and isn’t a trained to provide input to an aircraft flying by with an anomaly and ultimately will not provide, as far as I am concerned, actionable information.
I’ve also never flown nor practiced in the simulator a flyby in a commercial aircraft. I’ve also never landed partial gear nor practiced it in the sim, but a flyby would be optional, landed partial gear wouldn’t.