That floorplan was just a rough outline, and left out a LOT of details.
A finished plan would or should indeed include air filtration for both the side rooms- as you noted, dust control in the wood room, and grit/smoke control in the dirty room.
Other details would be things like the possibility of a sink out in the main area, for handwashing and parts rinsing, a floor drain, built-in compressed air manifolds- and for that matter, a room in the utility area specifically for the compressor, which would be cooled and soundproofed.
You'll also need to figure out how many outlets to have, including plenty of 110V, 220v 20 amp, and 220v 50 amp. Will you be including any 3-phase machines, wood, metal or otherwise? Generally 3-phase is expensive to both hook up and operate, but if you have the machines and the need, it can be quite valuable. If I had the chance to "do it all over again", I'd wire the shop for a selection of 3-phase drops, and install something like a Phase Perfect.
Will you want any fixed workbenches and cabinets? In-floor heat or overhead hot-air? Will you need AC? If you're planning woodworking, would it be worthwhile to build dust-collector ducting into the walls and/or floor? Do you plan a car lift?