I am currently having a similar issue. I have my GCS telemetry radio (RFD900) connected to telem1 and companion computer running DroneKit connected to telem2. With dronekit running on the companion computer the GCS failsafe does not trigger when loosing connection with the GCS radio. I have tested this on the ground by starting dronekit and powering off the GCS radio. The plane stays in Manual mode and never goes into RTL. If I turn Dronekit off and power off the GCS radio, the plane goes into RTL and stays in RTL after reconnecting the GCS. Is there a way to handle GCS failsafes differently on each telem port or another work around? If not, I would propose adding this feature as this seems like a major limitation for any flight with a companion computer and without RC such as flying BLOS.
Currently the only work around I have found is to send a request data stream message via mavlink as described here which would require a significant code rewrite on the companion computer.