In the example with the PF Baswood and the 3D settings, the areas that were black were just completely eaten away by the laser . I’ve attached the image I worked from so you can see what it looked like. I made some adjustments to it so the dark areas were true black.
If you check this link you’ll find a bit more info about it. It was my first time trying the 3D option and we talked a bit about it cutting all the way through the wood in the darker areas.
I’m never sure of someone’s understanding of file types etc., so forgive me if this is old news to you. 
If for some reason the 3D setting aren’t cutting out the areas like you want, you can add separate vector cut lines to the file to make sure the areas are removed. You just have to open the rastor image in a graphics program and either trace the image to get your vector lines or hand draw them. It’s more time consuming, but it guarantees areas are cut out.
My brain works in pictures so here ya go…
