This message was posted on behalf of Intel Corporation
On the Intel Aero RTF Drone, we use EKF2 by default as you mention because its much better on handling vibrations. When we changed to EKF2 the drone was tuned but this was not done with LPE.
Which software version are you using? You may see better results using the latest image, but as I mentioned we have not done any work with LPE.