That's correct. I'm deselecting all the operators while performing the package wizard. What's the point of deselecting operators there if they are included anyway in the final package? These operators were manually added and are operators for production employees to perform work with the application, none of those operators were actually used for any development or rule creation/modification.
I just tried it on my system and saw the operators included because I had 'Include associated data' checked for the Application in the Product rule. If I deselect that option, then the operators are not included unless I specifically add the individual instances.