It’s essentially cutting a 2D path with with an angled cutter. Picture a 2D drawing and a mirror image of the same on two pieces of paper. When you flip one on the other, the lines match up.
By manipulating the start depth of the male piece, you’re adjusting the depth at which the cut actually matches the original profile. If you don’t drop that start depth, the profiles would meet at the surface of both workpieces (like the paper). Setting the depth below the surface essentially ignores the stock above that point. That allows you to mate the pieces together, with control over the max depth of the insert.
It makes sense in my head, but I don’t know if, without a visual, my explanation here makes sense.