TxTallGuy--I don't know how basic or elaborate of a response you want so here you go. Basically the more advanced (degrees before TDC) fuel is ignited, the higher the pressure it is under and the more power the combustion can transfer to the piston. The reason to ignite prior to TDC is because of the time it takes for the ignition to occur, it is not instantaneous. By advancing the ignition the combustion is closer to the power stroke of the piston. However too far advanced and fuel can pre-ignite before the spark and work against the piston's power stroke. Lower octane fuel is more volatile and more likely to pre-ignite from heat and compression hence pinging or knocking. In this case the explosion is actually working against the power stroke of the engine. So there in lies the dilemma of advancing to the point of getting the most out of the combustion but preventing preignition of the fuel. Since the Rocket is lower compression and is timed to allow running on lower octane fuel there is some room to advance the timing and find the appropriate balance. So timing can be an important key to gaining the most out of the fuel you are putting into the bike.
The Rocket has four ignition maps. The labels wayne from tuneboy gave them is I 1, I 2, I 3, and I 4. I 1 is ignition timing for neutral, I 2 is for first gear, I 3 is second gear and I 4 is third through fifth gear. The timing is more advanced in I 4 than in I 2&3. By copying the ignition map from I 4 to I 2&3 the timing is more advanced thus translating to more power obtained from combustion. Triumph retarded the timing (detuned) first and second gears to smooth power delivery. With Toystoretom's bike he had the secondaries already removed and he had a PCIII installed which he has had good luck with and wanted to keep. So we loaded a stock Triumph tune with the ignition mods I mentioned earlier. He noticed a very appreciative gain in power and response. I hope they also explains why you would want to remove the restrictions.
DougL--I think wayne retarded the ignition in the #2 cylinder on the 20030_3 map for some reason or other. He added some fuel because it was leaner and he thought the decel popping was coming from there, and if it was too rough or jerky at small throttle opening because of the added fuel he may of retarded the ignition to smooth it out a little. To me that tune seemed smoother and power delivery seemed a little later but he had his best results on the dyno with it. Could be too because the bike was fitted with another product he sells.
Any of the mechanics out there (Tom) feel free to chime in with a professional opinion.