A unique feature of SMSim3 is Stored Pilots.
In this mode, you do not compare against the pilot as defined in the file. You create a Pilot file, and always use it instead. The reason for this is that especially with some of the new Low Frequency Custom sweeps used, it is possible that the recorder could accidentally select the wrong one if several have been defined (say for testing).
If they are all the same length, and roughly similar, this mistake can go unnoticed, and in processing sims, if using this incorrect pilot, the sim will look OK, but will in fact be the wrong sweep.
Using a Stored pilot means we can catch a mistake like this as we will be using a trace that is independent of the file.