Hey Turbomiles,
Having used both, I can tell no difference between the changes which must be made offline and then flashed for the 48 and 128. What the tuner is referring to is, after flashing your newly compiled software to the ECU (offline changes), you must key the ignition off and wait 60 seconds before keying on again. In this time, you hear the ECU switch off the main relay. Both the 48 and 128 do this.
To answer your question, yes, you can write to both the 48 and 128 real-time. The majority of your tuning (fuel VE and spark maps) is done online and instantaneously. Offline changes for matters like pin assignment are things that, in my opinion, would not waste dyno time because you or your dealer has already taken care of them while pinning out the harness and getting the vehicle moving under its own power.