"There is one thing I don't understand: if Luciano was in no way superior to other bosses, then why did the government free him and why did they deal with him and not the other bosses when organizing the landing of the army in Sicily using his mafia contacts?"

The governor of New York at the time (Dewey) was looking for contributions for his upcoming presidential campaign. Simple as that.

Luciano most probably had nothing to do with the landing of the US Army in Italy. Besides, Lucky had no contacts within the Sicilian Mafia at the time. Read Tim Newark´s "Lucky Luciano, the real and the fake gangster".