The Z height of the boundary "artwork" has NO effect on how deep the toolpath goes. Sounds like you "intend" the tool not to go "deeper" than the boundary - but you can not specify it that way. Set your depth in the tool parameters for that operation instead. Think of the boundary as an "infinitely high wall" rather than a line... As stated, though, I agree that "sometimes" the boundary affects the diameter of the tool, and sometimes the center of it - I have not looked in to which applies when... If it simulates "wrong" I edit the boundary to make it "right".
That said, does your model have a sharp corner on that edge? If so, it should not be "gouging" in to that corner. If you have the chamfer in the model, I suggest you edit it out and use the "full size" for cutting the part, and add the chamfer as a CAM operation only...
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