The logic is simple. The club is the RFL member, so if the owner of the club suffers an insolvency event and not paying players wages is surely from the RFL point of view top of the list as such an event, then the club gets penalised not the company. Consequently a new owner therefore buys a club with 12 penalty points, although if they offered to pay off all the debts those points should not be deducted, and not the case here.
The RFL articles of association List of Members lists first of all each club eg Bradford Bulls and then alongside the owning Company, Bradford Bulls Holdings Ltd in the example I am looking at. Take a fixture, and you will see that it is Bradford Bulls versus Leeds Rhinos, not Bradford Bulls Holdings Ltd versus Leeds Cricket Football and Athletic Company Ltd.