The spacers are used primarily for 2 reasons - one is simply to create more room tall valve covers. The valve covers are often needed to clear certain rocker arms/valve trains. Second is to thermally isolate the upper from the lower - making it possible to more easily ice down the upper intake between rounds which theoretically keeps the manifold from heating up the air intake charge as much as it otherwise would - which helps power. To perform this function, the spacers are made out of some composite, non-metallic material - usually reinforced phenolic resins. The spacer also lengthens the manifold runner length which, again theoretically, shifts the power curve slightly - all things equal, a longer runner makes a bit more torque lower, a bit less power.
As a practical matter, most people don't notice any difference at all except that their manifold/throttle body clears their valve covers. But it's a good CNC project provided you use the right material.