Using ArduPilot and Pixhawk for pose estimation only?

Hi all,
I hope this is the right place for this question.

I am building a prototype of a self-contained payload that will be mounted on a multicopter (that already has it’s own autopilot, etc.), and need position, altitude and orientation estimation. While I know I can get my own sensors and use something like EKF, at this point I prefer to use a proven implementation just to get things started faster.

Since I had good experience with ArduPilot, Pixhawk and the EKF module, I was thinking of using ArduPilot in a “read-only” mode, i.e. use it only for sensor processing and pose estimation (with MAVLink output) but not to control the aircraft. Is this possible? If so, what would be the right way to configure and calibrate the “read-only” ArduPilot/Pixhawk?

Thanks in advance.