It is not so hard to guess.
Changes are propagated automatically during prepare phase.
So run and patch fs are synched. We are getting ready right? Anyways; for instance; now, think about a change that you or a patch that you apply in EBS 12.1.
You follow the readme right?
Readme sometimes says; "run autoconfig" at the end.
So, this is similar.
Patch fs is like a separate EBS instance.
When you synch it from run fs, you actually patch it.
So, autoconfig is a good thing to run there automatically, for the patch fs, and that's why it is present in adop prepare phase. (for the changes that may require autoconfig)