Safety LED details

How is the actual multicolor LED on Pixhawk GPS units implemented? I can see a single line on 10P GPS1 connector. Is it PWM controlled over this line or is it some kind of I2C over the shared bus with Magnetometer?

PX4 supports both. It depends on what drivers are enabled on the board you are using and the implementation of GPS.
You can see all light-supported drivers here:

If they follow the connector standard DS-009 Pixhawk Connector Standard then PIN 7 is one color safety led controlled by GPIO Up/Down.

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Then RGB LED needs to be controlled over an I2C bus.