I’m a bit confused about what you’re trying to do here. If you have something which can output independent PWM signals then you should be able send them as desired to the ESCs, in which case you can control each motor independently.
What kind of control board are you using? Pymavlink sends MAVLink messages, not PWM signals, so are you using a Pixhawk autopilot board, or something else?
Also, are you using our Companion software on your RPi (our standard Companion software only runs on RPi 3B, so unless you’re using Companion Beta there may be issues with this approach), or do you just have a Raspberry Pi that you’ve downloaded pymavlink onto?
If you’re using a standard setup of RPi3B + Pixhawk + normal Companion software, this comment is likely relevant: