I think it is fair to say that modern engines do not run at the best they could perform due to regulatory standards - mainly emission and noise. As we all know, new engines run very lean, especially in the reve ranges where emissions are measured. Carefully adjusting these setttings are not likely to do any harm to the engine (if the person doing it knows what he or she is doing, of course). Short of owning a dyno, the combination of a Powercommander with an Autotune module has been a good solution for me.
The question of tuning a Rocket 3 to me is not primarily about more power. The question to me would be: Is the stock engine already the best it can be? Or is it limited, strangled and de-tuned - and desperately longing to be freed?