You may be overthinking this.
You are setting your Z zero to the top of the material. According to your post.
If the dialog shows your model some distance below the top of the material, then that is what will happen unless you move the little slider and make the model go to the top.
Most folks either put the model at the very top, zero gap, or .015 or so gap to make sure no mysterious flat spots appear because the stock is not uniform.
I have never been sure where some of the larger gaps come from, but I think they appear after fiddling around with model thickness controls....never bothered to really find out because I usually set my gap to .015 and do not worry about where it came from.
I find that I have far fewer headaches if I do not try to figure out where some number I am not interested in came from or how it was calculated, I just do not care, I know what I want the gap to be so I set it to that number.
Edit: The highest point in your model is at zero if you set the gap to zero. Sounds strange, but you can create a component, a pocket that is .25 deep and the thickness is .25. So far, so good. Then drop another component on top of it and make that component .5 thick. It will look like the second one is above the surface. But when you set the gap to zero and machine it, that first component will be .5 deep, not .25. If you give that a try it will help in wrapping the brain around how this all works.
Low Profile CNC Router Vise