Hi Alex,
serial5 can now be used not only as a debug, but as a serial port, as outlined here https://discuss.ardupilot.org/t/serial-5-pinout-on-pixhawk-2-1/29392. and here https://github.com/ArduPilot/ardupilot/pull/6761.
Plus, the unexpected behavior as outlined above happens, whether SER5 is active or not.
Could this have to do with the Frsky passthrough protocol in some way?