That spec of being above the top of the secondary doesn't take belt variance into account. Very often you get a belt that is just a little shorter than spec, so having the belt above the secondary will cause it to squeal at idle. You can adjust per the specific belt though.
The higher up in the secondary the belt sits, the more engagement and bottom end torque you can get down to your driveshaft. Makes absolutely no difference once it starts shifting though.
Height in the secondary is adjusted by adding or removing washers from the 3 bolts in the back of the secondary.
Re ridge in the primary..... normal, but not good. OEM belts are very hard and tend to slip, causing friction and wear on the surface of the clutch. Keep an eye on it, and when it starts looking really bad or you start getting cracks in the face, it'll be time to replace the sheaves.