It is actually the difference between the top end and the bottom end which controls the relative lengths of the lines. Thus holding a bit lower just means the bottom moves a little less while the top moves enough in the opposite direction to make up for the amount the bottom doesn't move. Do the math and you will see that the difference (total motion) will be the same for a given angle no matter where you hold the handles. This is for a given handle length; as CodyG's image demonstrates, longer handles equate to more motion-per-angle-change.
The one change when adjusting where you hold the handles (and it is very small) is that with a top-hold you are having all the motion occur at the bottom end and means that you are slightly loading the bottom of the sail as you change angle in the braking direction, whereas if you hold the handles near the middle, you will be doing less loading of the bottom of the sail and slightly unloading the top of the sail. This is such a small amount (inches) compared to moving your arms (many inches) or taking a step forward or backward (a foot or more) that it can be ignored. If you want to load or unload the sail you won't be doing that by rotating the handles.
Changing where you hold the handles just changes which muscles you are using to hold (in a steady position) or to rotate the handles. Holding the handles so there is no tendency for the line tension while in a hover to rotate the handles (you just pull the handles toward you). Holding higher (thumb on the top end) means you have to exert effort to pull the bottom more than the top (while in a hover). The muscles that control your ring and pinky fingers, and the muscles that rotate your whole hand toward the pinky will be under constant tension. Some like this, because it means you don't have to make the transition from no muscle tension to muscle tension. I suspect that it makes your reaction time a tiny bit quicker, and may also provide better feedback about what the kite is doing. I also suspect that the muscles that rotate your hand down are a bit stronger than the ones that rotate it upwards. I know that a mid-hold will soon result in sore muscles along the top of my forearms. The most comfortable hand position (for me) is with the thumb being a nearly straight extension of the forearm and the fingers angled slightly down.