I don't believe there is an
add_filter() call anywhere. If you want to override the option defaults, you can call your own
add_filter() to do so, either in a Plugin or in a Child Theme.
apply_filters() call is nothing more than a filter hook definition: basically, it is defining the data to which a filter hook is applied.
It is similar to
do_action(), which is an action hook definition: it defines the template location/runtime execution point at which the action hook is fired.
So, the presence of
apply_filters() does not imply that there will necessarily be a corresponding
add_filter() call; rather, it merely means that a filter is available to modify the specified data.
On the other hand, the presence of
add_filter() does imply that somewhere, a corresponding
apply_filters() call exists - just as the presence of an
add_action() call implies that somewhere, a corresponding
do_action() call exists.