That's not something that needs to be measured externally.

Also, one wonders just how horrible their production tolerances must be if something like this even needs that sort of calibration in the first place. No other company does this. Nonetheless, even if one accepts this bizarre excuse at face value, it doesn't take a genius to realise that the firmware can "self-calibrate" trivially: If the EEPROM in the sensor is uninitialised, then it just needs to record the max/min value the first time it's closed, and save that as the "lid closed" point.

The only plausible explanation for doing all this extra work is that this isn't merely incompetence; it's intentional malice. Given how much Apple spends on lobbying and other hostile activities, this is not surprising.

How would you know the user is ready to perform the command?

It does actually perform a security function. The lid angle sensor is used to know when the device is open or closed, and when closed, it physically disconnects the microphone. If you were to be able to recalibrate it at any time, you would leave your device vulnerable to having the microphone enabled when the lid is closed. You can argue whether that justifies the practice, but it's not as simple as just burning the EEPROM serial number in that tells it to turn the display on or off. It defends the user against an attack vector.

From that perspective making it one-time programmable is not unreasonable.