There are number of authorised Local Rules where a LR seems to be contrary to a substantive Rule.
In these cases the Ruling Bodies have recognised that in specific situations the substantive rule is neither appropriate nor desirable. In these limited cases the RBs have approved/authorised a Local Rule. The RBs are the only body who can authorise Local Rules.
Sometimes outside organisations (clubs etc) may have a particular issue which may be unique to their course. They may contact their appropriate RB who might give them a specific authorisation fro a Local Rule.