In what way do you believe the Reference Amp is important? As far as I am aware the reference amp is actually the amp you are profiling.
The starting amp in the KPA is only used to speed up the creation of meta data tags such as amp name and speaker type etc by prepopulating these fields from the loaded rig.
I believe that the default Crunch rig created by ckemper is the “reference” for all profiling regardless of what rig you have loaded to prepopulate tags.
I’m referring to the output volume of the reference amp while it’s being profiled. By varying the volume it affects the profile in several different ways.
As far as the starting rig I haven’t noticed that it matters what it is