I have some artwork setup to start my first cuts tomorrow. I’ve gone through the settings over and over and over again. I imported the tool profiles for the Amana bit I am going to use, the 46200-K and in my project settings, when I have the stock thickness zero height set to top, the simulation doesn’t look like it cuts all the way through. When I have it set to bottom, it does. I’ve not found a definitive answer on this, but just info about some bits not being able to do it correctly.
Pretty sure it’s a CC preview issue only. I have had cases where the preview showed the cut as not going through, but increasing max depth by a hair fixed it (which you may want to do anyway: if you’re one of the folks who use their wasteboard as a wasteboard, then it is beneficial to overcut by some margin)
Where you set to zero should not matter, and it’s probably just a slightly different rounding in the math that makes the preview correct or not. I don’t believe the tool definition matters either, for a square endmill max depth is max depth, whatever the endmill characteristics are.
If you’d rather make sure you don’t cut (at all) into the wasteboard but still go through the piece, that’s when setting zero reference to stock bottom shines, regardless of subtle differences in actual stock thickness.