1) I almost always skip the wizard myself, so I had to make a quick check. I think that the specified sort order becomes a step in the script that is also created if you specify the "create a script" option.
2) yes, you can enter layout mode and make further changes to your layout design. You almost always have to at least "tweak" the layout design generated by the wizard anyway.
3) If you are new to FileMaker, it can be a very good way to pull together a basic working layout for a commonly needed database task.
But, IMO, the more familiar you are with FileMaker and how a layout can be designed, the less useful the wizard becomes. I find that what I need to have on a layout tends to "evolve" as I complete the design and work with the client to understand what they need/want/like anyway so I often create a simple layout and then enhance it periodically as the database design reaches the point where I deliver it to a client.