Politely ask the engineer for the exact code references. Do not accept "It's in the NYC electrical code." You want chapter and verse. He won't be able to find it. Now you can start the real conversation.
For what it's worth, virtually nothing he said is correct. NPLFA wiring certainly doesn't have to be 2-hour rated, in rigid and in a 2-hour rated enclosure. IFF you have a venue where total evacuation is not employed, then certain aspects of Pathway Survivability come into play. Notification pathways may be required to have a 2-hour survivability rating (PS Level 2):
12.4.3 Pathway Survivability Level 2. Pathway survivability
Level 2 shall consist of one or more of the following:
(1) 2-hour fire-rated circuit integrity (CI) cable
(2) 2-hour fire-rated cable system [electrical circuit protective
system(s)]
(3) 2-hour fire-rated enclosure or protected area
(4) 2-hour performance alternatives approved by the authority
having jurisdiction
You pick ONE, not all of (1) to (3).
Now, if he was talking about the wiring on the line side of the FACP power supply, AND you are in a PS Level 2 situation, then NFPA 72 requires that the power supply line-side conductors have 2-hour fire protection:
10.5.10.3.1.3 Where survivability of circuits is required by another
section of the Code, equal protection shall be provided
for power supply circuits.