Good question. I tried the M2.5 screws, but they didn't fit the board snug and it "rattled" around. The M3 machine screws I used self-tapped themselves into the PCB and into the plastic, though you do have to put some pressure to make sure that the board seats down. I'd recommend screwing in the nut without the carrier board just to tap it first too. Any design suggestions would be appreciated on this too.
For the NanoMesh Mini design – https://www.thingiverse.com/thing:3547555 I went with PCB stanchions with little nubs to hold the carrier board without any screws. Because of that case design, it wasn't as important to screw it down.