3D toolpaths cut deth should be to the bottom.
There are two exceptions.
1) If the tool won't fit in the pocket, it won't be ablt to cut the entire depth.
2) If the vector boundary does not leave enough room for the tool around the edges, then it won't be able to cut the entire depth.
You should learn to do this job using 3D vectors instead of from an .stl.
The toolpaths will be much more efficient, resulting in cut times of probably 10x faster.
And the finish will be much better.
Attach your .stl and V Carve file (zip them).