Agree some advise this, but I tend to follow what the manufacturer advises first and then if I find some evidence to contradict that I deviate. DJI doesn't seem to recommend IMU calibration on arrival or with firmware updates.
I am not saying it hurts anything if done properly, but based on what I have seen DJI probably has pretty specific conditions that they do the factory IMU calibration under. Those conditions are probably used for all their validation, testing, and troubleshooting. The main purpose is to learn the nuisances of all the sensors...those deviations do not change with firmware changes or typical shipping.
I used to have to go through the calibration process with some old school accelerometers and many times I would redo them over and over and over again as I can be a little OCD. Many of those times the first one was the best and I should have just stopped messing with it!
So in my mind I did not think I could get the Phantom in a better position than DJI to run the IMU calibration. Is it best to level it based on the skids being level or perhaps you want all the arms level, or maybe the circuit board?
So for myself I stuck with the factory calibration after reviewing all the sensor data....which I look at before each flight....