Map objects and labeling upon page load for folders that are automatically generated.

We are able to control what map objects and labels are visible upon page load for folders that we manually add to the map, this is great.  So is it possible to give us control over the visibility of folder map objects and labels upon page load for the automatically generated folders such as Markers, Lines & Polygons, Operational Periods, Assignments, and Clues?  If we can have that control over some folders, why not give us that control over all the folders? 

Thanks