From what I understand, you can't tune anything but full-throttle runs on an inertia dyno. And even that is only after the fact from the data logs from the brief period the engine spends at each RPM and load cell.
To do any real tuning, you must use a loading dyno to hold at any RPM and load to dial in that cell right there. And this is only after you drive it on the dyno to warm up the engine, transmission, rear end, etc.
I used to work at a shop years ago, but I wasn't the tuner. I just got free dyno time and tuned my own cars, and a few customer cars.
To those saying that dynos can't simulate real street conditions, that may be true that it can't match it identically, but the loading dynos can easily be setup to simulate worse than normal conditions, and that's what you should tune in. Hotter coolant, worse airflow to the radiator, worst case. That way when they come off the rollers and beat the **** out of it, you know they'll have a margin of safety--and can't come back complaining that you blew up their engine.
Intertia dynos are only for max-power pulls. A lot of the eddy-current modules are being added to them now-a-days as people realize this.
Also, the proper way to use knock control is to turn off knock control while tuning, but still watch the knock sensor output. Then tune without the knock retard kicking in (and offsetting your timing values) but still paying attention to knock, to get the best case (which may or may not be near the knock threshold), then when done they simply turn knock retard back on and let the computer retard timing as necessary on the street.