A short addition to my previous post:
I did actually encounter a situation where I needed non-zero collision margins lately:
Trying to stabilize a physics simulation with small objects (around 10cm / 0.1 BU) gaining some speed by falling, I had to modify (raise) the value for the margins. With a zero margin the mesh collision objects where passing right through the floor.
Considering this, it might be actually beneficial being able to set specific collision margins for physics objects (mesh and primitives).
The only thing that actually helped, was setting the collision margin in combination with applying high angular and linear damping to reduce the speed.
I do not know if this is a proven way of stabilizing physics collisions with ammo.js, but up to this point I haven’t found another solution – open to any suggestions, as usual.