Like what has said above, the anodising process coats the whole rim. Depending upon the rim, this is either left on, or machined off to an extent. Some just take the paint off, others - Mavic etc. use additional processes to make sure the join is totally smooth as well on their better rims. Mavic have a new rim finish Exalth, that isn't machined,but has a special finish to maximise braking on top end rims (light weight also) but it remains unknown as the anodising wears off does it look a bit 'scruffy' after use ?
I have some Mavic Open 4's that were anodised fully, the brake surface has finally worn through the 'paint' now the rims have ended on the commuter, so looks neater rather than dark grey/alloy scratch type finish.