Fix overriding the permissions visibility for a document type, the new visibility for a permission should override the default one on the given document type

The current logic allows to contribute a set of visibile items on a document types, but these are merged always with the set of default permissions ( and the default permission "weight" more, so their attributes are kept as a result of the merge ) . The sense of the merge should be the other way around, the new visibility for a permission should override the default one on the given document type.