I did a few flights with two EKF3 cores enabled (IMU0 and IMU1) using a Pixhawk Cube Orange. Then, I compared the output of EKF3 cores (XKF1 vs XKF6). The output is very similar for both cores, except for the altitude (XKF1.PD vs XKF6.PD):
Both altitude match pretty well but there is a constant bias in the order of 30cm to 1m depending on the flight. It seems to be more an altitude initialization error of the second EKF3 core rather than an estimation problem in itself. Any clue?