In the long term, mixing life-safety fire alarm fiber optics with BMS (Building Management System), which is not life safety, becomes a huge issue because people working on the BMS can accidentally disable the fire alarm system, and then the fire alarm system needs repair.
Electrically, there is no problem with running fiber anything in the same conduit as anything, including low voltage DC, household or commercial wiring, or even inside of high-tension power transmission lines that go across country. The only concern is that if the fiber is metal jacketed, proper grounding procedures have to be complied with.
But that's not the issue with the engineers.
People in most walks of life are afraid of fire alarm systems. They're afraid of sounding the alarms, and they're afraid of a vague "something-bad-is-going-to-happen-if-I-touch-it." There are, of course, exceptions, but this is the general attitude toward fire alarm systems.
On the other hand, electricians, HVAC people, building maintenance people, other low voltage trades unfamiliar with fire alarm systems are not afraid of standard building wiring, including BMS, security, cable TV, data, etc. Any wire run (or fiber optic run) inside conduits for their system is fair game to mess with.
Short term, there no problem with mixing fire alarm with other systems. Long term, mixing life-safety fire alarm with BMS, which is not life safety, becomes a huge issue because of the accidental disabling of the fire alarm system and the subsequent needed repairs.
Right now is the best time, as the building is being put up or remodeled, to separate the systems (I assume that the owners aren't concerned with cosmetics as extra conduits are installed). Without the separation that the engineers want, the system will be a constant maintenance headache.