If you enter a negative 0.75” as a material thickness after spoilboard touch, and your material is thinner than that amount, your pocket depths would be shy by the difference between 0.75” and the actual thickness of material. Same for rasters - you’ll end up with “flat spots” and any material allowance between Roughing and finishing will be incorrect (areas near the surface of the material)
I’m also puzzled why your machine is not lifting to a safe Z Height before moving to your XY zero position after spoilboard touchdown? (if you don’t enter the negative Z)
After all said and done, It's best not to be lazy and measure the material before setup, but for fun, go measure the thickness of a board at different places and I bet you'll be off a few thousandth at the different places.
You're right if I'm doing pockets and that's the exception where the pocket won't be as deep, however "most times" the material difference is only a couple thousandths, so unless you're doing inlays, that's really not big a problem. However, the majority of time I will measure the material before setup and if the material is the same as my setup, there won't be an exception.
The majority of my projects over the past year or so has been Double-sided models, so I am less concerned about what I've cut or not cut above the model as long as the model turns out the right measurement. Correct setup matters, but if the material is thinner than my setup, my model will be off if I zero to the lower height, especially notable in thinner areas of the model. As far as roughing and finishing, I don't see the problem. The finishing will just take less material, but the outcome should be the same (I usually leave material higher and lower than the model at setup, so flat areas are not a problem). So to clarify, I'm only talking a few thousandths here and there.
My machine does lift to a safe Z Height, however, since I do not have an automatic tool changer, I move the spindle to the front of the machine so I can easily change mills, then bottom it to the spoilboard, put a negative height as mentioned, raise the spindle higher than the material and hit the "Go to Zero". My reasoning is I don't want it to drive through the material finding zero.