Thanks for more insightful observations, i will have a look on harmonic notch filter feature, i know barometer on f405 custom board having some issues, but don’t think that contributed that much during the arming and takeoff phase EKF innovation variations, one thing it seems like in all the cases that, over time when FC board temperature rises and after the arming and takeoff phase, sudden fall of temperature seems to be causing some unwanted noises on IMU. Not sure if that is playing any part in causing this issue.
One more thing which i worry about to keep flying when that scenario repeats again is that EKF/IMU might not able to recover from this once its starts getting high EKF innovations as happened in this case Continuous uncommanded climb, suspecting EKF issues, that’s why i am looking what can be safer options which can be in place from the firmware or failsafes end during that scenario.