Thread size and standoff height are specs, not afterthoughts. Discovering the M3 screws are 2 mm too long after the enclosure is drilled adds an unpleasant errand to a finished build.
M3 and M2 screw-and-nut sets, nylon and metal standoffs, LED holders in 5–10 mm, and DIN-rail PCB holders. Adafruit's M3 nylon stand-off set and Pimoroni's Pi standoffs handle the most common Raspberry Pi stacking heights.