Yes, I guess you are right. But was trying so say: todays safety in aviation has been achieved - among other activities - by deep analysis of accidents and drawing the right conclusions out of this. Basically because to stop a flight is not as easy as to stop a car.
Additionally, accidents are seldom a result of a single failure, but a combination of several. So arduino might be fine, but im combination with others probably not - if not mitigated.
Coming back to your question. Reliabilty of (PWM-) transmission depends on susceptibility of your design including wiring for external electromagnetical threads; both radiated and conducted. And then it is not only about the signal itself but also used hardware that sends the PWM signal and picking it up.
PWM is a asymmetric signal, thus more susceptible than symmetric signals. But, honestly, giving advise a little difficult. By nature, asymmetric PWM is not the best choice. Think about symmetric signal transmission. Or proper shielding and bonding of your signal, including connection of motor and arduino itself. And, oh, proper grounding/bonding concept for the whole thing.