Hello Paulo,
The auto setting for the number of time steps or “Run for…” setting is it is the number of time steps required to get from one corner of the simulation domain to the opposite corner if it were traveling through the highest refractive index material in the design. it is not meant to reduce the reflections as you are correct this is the role of the PML that is defined at that boundary.
As with any auto setting it is merely a good starting point to get the simulation running. This is one of the reasons we almost always recommend placing an observation point where you are going to be extracting information and looking at the time domain information to ensure that the power has fully propagated through the structure (for CW – reach steady state and for pulse – power decays to zero).
Scott