They should be the outputs for encoder and keyboard keys leds. The settings are in the Options->Panel menu (see the attached picture).
For what I know the E-Coder protocol is not open, but you could consider using the TCI protocol.
In a few days I should publish a Arduino (ESP32) library that cover almost every 1.3 TCI command.
You can use it for everything you need.
In the second picture you can see a typical application: an automatic band switch with hw com port for each receiver.
I also thought about using TCI for this task but as far as I can see that necessitates a listener between the eesdr and the usb-based peripheral (ie. an alternative e-coder). On the other hand that solution could provide extended functionality over the original e-coder!
I would be VERY interested in seeing your implementation of the Arduino TCI-library (I’m almost solely use STM32 but it shouldn't be a problem porting it).