That's kind of a red flag on that Fire/Burg company. But like you said, that's going to be someone else's problem.

I know in Chicago everything has to be in EMT. So even your LV all had to be in metal conduit. That raises the pricing considerably.
Again, someone from NY would need to chime in to know if it is the same in NY city, inside of High Rises.
But either way, I would check with the general contractor about this. And if they shrug their shoulders, then check with the JHA. And hope that doesn't cause an issue where the general contractor usually gets away with a bunch of stuff, but since you got the JHA invloved early and he's seen it with the walls still open. NOW there's an issue and everyone is pissed at you for trying to do things right.

Again, just things that I've heard over the years about the way things get done in NY.