Why does Uranium ignore the General Options of the backup set?

The General Options of the backup set only affect the copies performed inside the Common Destinations.
So, you must enable the copy to the Common Destinations in every element of the backup set if you want the General Options to be applied.

Note: the General Options of the backup set only affect the copies performed inside the Common Destinations. The main destination of the elements, configured in the specific Wizard for creating the element itself, will not be affected.