this is because when the factory produces the engine parts, the
bore of the cylinder and the piston, they try to make them fit as
nicely as possible. but it is impossible to make a perfect seal,so
what happens is that the diameter of the bore and the size of the
piston is something like can fit properly but not the optimum
fit.
so when the engine starts, the pistons 'grinds' aganist the
cylinder wall. they sort of 'sand' or 'smoothen the surfaces,
something like using sandpaper to smoothen a piece of wood. then
the tiny metal particles are carried by the lubricants.
the idea of running-in is to achieve a optimum seal between the
cylinder wall and the piston with a thin layer of lubricant between
them.
when there is a very good seal, the gases inside the chamber would
not escape and no energy is lost this way.
anyway the reason why there is a air filter ( and oil filter ) is
to remove as much solid particles before pumping into the engine.
because if there is, then it's byebye for yr engine.