Option 1 is the preferred one, because it involves fewer body parts.
In the old days of basketball, people would not jump at all for game play shots, and use the Korac-style two-hand shot from the knees for free-throws, also known as "grandma style". Underhand, with both hands down. He held the ball between his legs, one hand on each side.
But with defenses getting better, it ended up being an advantage to do your shot from as high as possible, hence people started doing the over the shoulders shot, then incorporated the jumping-then-shot over the shoulders technique.
The reason why it's better to (1) first jump to the highest point and then (2) shot when you are at your highest is because you can isolate one from the other. By isolating the jumping motion to the shot motion as much as possible, it is easier to train by repetition. This means that you can train yourself to a shot motion from your shoulders, arms and wrists, and the motion will be the same when...