Navigator WebAssistant is an alternative way of interfacing with our Navigator flight controller, which directly communicates with the onboard sensors and peripherals instead of going via an autopilot firmware.
If your board has the same pinout and components as our Navigator then (after disabling your autopilot) you should be able to use the Navigator WebAssistant to confirm whether your PWM outputs are working as expected.
If they work there then your issue is likely with the ArduPlane firmware version you’re running (e.g. it may not have the Navigator board defined), but otherwise there may be some issue with your Raspberry Pi configuration, or with the hardware of your board (e.g. the routing of connections to or from the PWM chip, or the chip itself).