Can you be a little more specific? Power limited cable, as a rule, doesn't have to be MC/AC or run in a raceway. Is the spec or design calling for RMC or some such? Are you worried about the serviceability of the fire alarm devices (can be an issue with tamper and flow switches, for instance)?
Device protection? Do you mean protecting the cable?
Regarding the height of a FA cable all you get is:
760.130 B(1) "...when located within 7' of the floor, cables shall be secured in an approved manner in at an intervals of not more than 18".
If it was in the elevator shaft then 760.130 B(3) says it must be in conduit or EMT.
Personally I would not have an issue with MC cable in the machine room because its normally locked up, but a little greenfield never hurt my feelings. We use the reduced wall 3/8" FMC to sleeve 14/2 FPL in sprinkler rooms etc. I got flack from a couple of inspectors thinking its MC, they wouldn't allow it, local thing. I had to carry around a piece of MC on inspections to show the size and material difference. Its actually a hilarious exercise, the inspectors that look that close hate being proved wrong in two seconds, but I do it nicely.