Top Height relative to Z-zero

[epic41]

I have been looking through the documentation for Fusion 360 (it is frustrating to not have a dedicated manual) and I am under the understanding that whatever you set your 'top height' to in the CAM module of F360 becomes the Z-zero you set in your machine, is this correct?

I am running a Shapeoko 3 with a Grbl 0.9 controller and I am zeroing the Z-axis at the stock top, then setting 'top height' to stock top (stock has been properly represented in the main 'setup' dialog), but when I go to cut the g-code that is generated corresponds with what would be 'bottom height' as Z-zero. Is that the way it is supposed to be?

I have a 19.05mm mounting board that I am trying to cut holes through: the top 10mm has an enlarged 6mm diameter for threaded inserts and the remainder has a smaller 4.1mm diameter for excess #8 screw length past the insert. My 'origin' in the setup is set to 'model origin' which is the bottom-back-right corner (using the naming convention on the 3d-cube). Z-positive is movement upward toward the viewer in the attached pic.

The Z-zero is off by exactly the stock width so I know I can type in offsets to the heights in the CAM module (or reposition the setup origin), but it seems that the stock-top touch-off point I set as Z=zero in the shapeoko 3 would be the logical choice for the CAM to make Z=zero (via the 'stock top' selection in 'top height'). If not, doesn't it make it more difficult to compensate for excess stock outside of the model (one cannot use that as a set point for setup origin)?

Please help me out and pardon any mis-understanding I may have concerning Z-height in F360, thanks!!

[LibertyMachine]

Your G-Code XYZ values are all based on the location of your WCS. If you have defined the WCS as the bottom corner of the stock or part, that is where it's going to pull the numbers from. The Heights tab controls how far and where it rapids or feed to

EDIT, with pictures!  Your existing choice and selection:

Perhaps a more proper selection: You really want to get into the habit of always selecting Z and X axis, as I've done in the below picture. Reason for that: The model won't ALWAYS be oriented properly. It will cause you grief. I also prefer to choose my WCS location: