40mm fan mounted with M3x5x4 inserts, does not constrain pins header.

There's not much to add. I did not have M2.5 bolts until recently so I simply re-drilled the Pi bolt holes by rotating the M3 screw there for a while everytime with no problems.

Height including the Pi is 15 mm, so 16 mm screws will extend 1 mm below Pi. 20-25 mm bolts are probably ideal, depending on what standoff you use.