Seems like the drone didn’t think it was already landed. Why that is I don’t know though.
You could try to set up an arming/disarming switch instead of using throttle input.
That it didn’t disarm when activating e-stop is normal, e-stop and disarmed are different states.
Also you could try to ask @Ramya for help, he/she/whatever had a similar problem recently and maybe found an answer already?
You seem to have two rangefinders configured to RNGFND1_TYPE,11 (USD1_Serial), RNGFND1_ORIENT,25. You should have used this for EK3_SRC1_POSZ after the UA is stable in flying with your three barometers (experience height drop). But, RNGFND1_MAX_CM,2000, up to 20m only.
Your YAW initial parameter setting for a 23" propeller does not seem correct. ATC_ACCEL_Y_MAX,7000
I do not recommend you rush to test the avoidance sensor. Have you completed the Harmonic Notch filter noise cancellation and autotuning?
Your UA z-vibration is still high.
you may want to revisit your MOT_THST_EXPO,0.77 and ANGLE_MAX,1000, and LOIT_ANG_MAX,15 in windy conditions. Your Arming check is weak.
You should consider upgrading the firmware to 4.4.4.
I recommend you to follow this guide.