After some more experience I’ve learnt the best way to calibrate the ESC is to NOT calibrate it! Use a firmware tool which is easy to use (e.g. BLHeli Suite or RapidFlash) and set the minimum and maximum within the range of your transmitter, which you will see on the RC calibration screen. For example for Taranis X9D we always have 982-2006 as the range with 1496~1500 at the centre.
You should add some PWM buffer at the top and bottom to make sure you can stop the motors and get full power or tilt without having to push hard. I prefer to keep the range 1000-2000 with 1500 as centre which is the default in many other flight controllers. The Taranis fits in there nicely. If you don’t have a Taranis and the PWM range is really skewed around different endpoints then you should set that into your ESC accordingly. I could adjust this a bit lower to be mathematically correct but there is a deadzone in the middle anyway and I like round numbers 
Once I had a situation where a APM was incorrectly calibrating some ESCs with different values or jumping into calibration mode when it wasn’t desired (on an old Pixhawk and old firmware, not on a Navio). Even when programmed directly they spun-up and stopped correctly, i.e. to the same PWM values. So I think only the old or bigger ESCs really have noticeable variations? On my 250 models I never had any discrepancies, so for me ESC calibration is not only un-necessary but worse, it introduces variance in the configuration and hides settings you should have under control (because you don’t normally bother to connect the ESCs again after calibration to see what the results were). For that reason I also disable the RC calibration feature to prevent unwanted changes/misconfiguration.
At the same time I’d recommend re-flashing SimonK to BLHeli if it is supported on your ESC. Besides a clear popularity swing away from SimonK (the opposite was true last year) the BLHeli firmware can read back the settings and manage them much better than the blind SimonK flash method (or did I miss some option to read the settings back in SimonK/RapidFlash?).
If you have a big multirotor then maybe somebody else has advice and calibration is still necessary.