Make landing autopilot account for true altitude

Mechjeb tends to crash my spaceships into the surface of Duna far too frequently due to the large discrepancy between the altitude given by the altimeter and the true altitude. It seems to spend time waiting to get to the right altitude for a burn that should have taken place two kilometers up, which never ends well. Mechjeb seems to be able to access data for true altitude, so might it be possible to try to make it account for that in landing?