RE: Reason for nocking point to be high and not square?
Although nock travel affects where the ideal position is, and so does riser design, nock height is most easily adjusted with tiller. You can move it up or down easily by adjusting tiller. However, most bows have the straightest nock travel, with it in a particular position. You should check with the manufacturer, or if you have access to a tiller board, you can figure it out yourself. Let's say the manufacturer says that ideal nock height is 3/8" above level, but your bow is set at 1/4" above level to get good groups. You can get it to 3/8" by adjusting tiller.
The reason nock height isn't identical on every bow of a particular model, is that limbs are not clones. Sometimes one flexes every so slightly more than the other. In this instance you have to adjust tiller to get the nock height into ideal position for that bow.