The question seems to be centered around who has more authority: the NFPA, or else the Authority Having Jurisdiction (AHJ). Our problem, being the ones designing installing and maintaining fire alarm systems, is that we're stuck in the middle.
The National Fire Protection Association, Inc. is a non-profit publishing house. They show the minimum requirements to have an adequate fire alarm system. The systems they show are "The least expensive system that anyone can get away with". The NFPA, also, is not a rule making authority.
Near the beginning of the NFPA 72 Code, the term AHJ is defined. In their definition they say something like "An organization, office, or individual responsible for enforcing the requirements of a code or standard, or for approving equipment, materials, an installation, or a procedure".
Even the NFPA knows they don't have the authority over fire alarm installations.
The fire marshal has motivation to protect people and property from fire. According to the NFPA, the fire marshal has authority over the fire alarm system, and for approving an installation.
Remember, the government makes the rules and laws that we live by. The fire marshal is a representative of the government, and may have more stringent requirements for an installation than the bare minimum standards shown in the NFPA Code. The fire marshal has the government's authority.
The NFPA has a book they publish that explains further the meanings of the NFPA 72 Code, including insights provided by the writers and editors of the Code itself. It's the NFPA 72 National Fire Alarm Code Handbook. You can find this Handbook right next to the NFPA 72 Code on the www.nfpa.org website
In that Handbook, the writers basically say that if an AHJ wants something more stringent than what is shown in the NFPA 72 Code, we, as the designers, installers, and maintainers of fire alarm system, go with the more stringent requirements.
Keep in mind that it's the owner's fire alarm system, not the design or installation company's system. Our job is to help the owner comply with the law.