The "Contained Collection Types" is used for the parent-collection types which may hold child-collection types. For example, Notebook is a parent-collection for the Experiment child-collection. When you need to add sections to the experiment, this is done via New Section FT.

The difference between "Contained Collection Types" and "Contained Collection Templates" is visible to the user when he creates his own templates in the User Configuration -> My Templates folder.

In case only "Contained Collection Types" is configured, the user may add only experiments of the allowed types but not his own updated templates.

In case both "Contained Collection Types" and "Contained Collection Templates" are configured, the user may add both types of collections -available experiment types and his own updated experiment templates from User Configuration -> My Templates folder.