In many countries, the company manual (FOM) is approved by the aviation authority of the country, hence violating the FOM can be interpreted as violating the law. Where as, manual thats accepted means violation of which is an internal matter.
It is like if a company has MEL, we follow MEL instead of MMEL, if an item is required by MEL but not MMEL which has failed prior to departure, dispatch such an aircraft would be an illegal action.