R/C overrride action

If I am issuing the R/C override every second (via Mavlink), will the Flight Controller still provide the actual R/C input values - also via Mavlink?

Basically, my telemetry channel is being fed through a companion computer, and at certain times the companion computer would take control via Mavlink to override the R/C input, but I also need to watch the R/C inputs for Chan5 MODE changes and Throttle/Yaw DISARM commands so that I can respond to those regardless of anything else.