The second phase of the deadlift starts somewhere around the knee, depending on your levers, but I prefer to define it in terms of the angle of the leg joints. This phase starts when the shins are perpendicular to the ground and the hips start to move forward more than they travel upward. During this phase, the quads have essentially exited from the picture and the weight has moved backward to over your heels, with the work being done by the hamstrings, glutes, erectors, and increasingly, the mid and upper back.
Eliminating the first phase by doing an isolation rack pull is a fantastic way of really focusing as much energy as possible on the back and 'wasting' less gas getting the bar up to this point. As such, it's great for a bodybuilder to use for back specialization and overall mass building, as it's probably the closest you can get to a full-back compound movement that includes the hamstrings and glutes.