The emphasis in the second pull should be hip extension and, just as important, immediate hip flexion. The object should not be to "drive the bar up by jumping". You are right to think it is a weakened position. Lifting is more like catapulting than jumping and emphasis in this country on the "jump and shrug up" model has held lifters back in the US. The major reasons for this are that when lifters try to jump to affect the bar they 1)move into the forefeet to soon and too much, leading to poor bar trajectory (more vertical or to the front) and 2) they tend to stall at the top of the 2nd pull hurting their transition speed to the receiving position.
The knee and hip extension work together to give the upward trajectory to the bar in the 2nd pull but the explosive hip extension(and quick flexion afterwards) is what puts the lifter in a better position in relation to the bar. That simply means that when the bar is accelerated by the hip extension, the lifter should immediately be in the business of getting under it, not proceeding any longer with a jumping motion. The hip/knee extension will cause most people to triple extend to some extent and jump to their final foot position for receiving the bar.
I also advise lifters not to shrug up as the completion of the 2nd pull but to use the shrug to help yourself descend.
Hope this helps.