Large scale manufacturing with many precise electrical parts, there is going to be some drift car to car but only one rom so the tuning has to accomodate all the expected variance.
You also have to remember there are no absolutes when trying to compare between different engines as design plays a big role. What works for a 4g63 is not going to work the same for a turbo EJ engine. Evo motors tend to run leaner (closer to 12/1) than EJs, but they also run less timing and have longer strokes and higher compression. A friends 951 turbo Porsche runs 12/1 under boost and has no problems because that engine is OK doing that.
And I would not look at what commercial tuners as the "best way" either, they have to cover their bases since customers blowing up motors is bad for business. Better to be richer and more conservative than risk a broken piston trying to eek out a touch more torque. I am always more conservative tuning others cars than I am my own, I keep a close eye on everything and my CEL flashes if I get knock but I know most normal people will just keep going if there is a problem.