Is it based on GPS altitude or baro altitude using standard pressure setting 1013 hPa. Is there a way to set QNH in-flight?
https://ardupilot.org/copter/docs/common-understanding-altitude.html
ardupilot calibrates baros for the local pressure on startup. post-startup adjustments are possible within certain limitations, in MissionPlanner press CTRL+F and look for the QNH button.
QNH is available in the advanced failsafe system too.
EDIT: just saw this PR: https://github.com/ArduPilot/ardupilot/pull/17179