So this is normal. Even in a standard render the intersection is not very clean until you add a multi-pixel filter and other interpolation techniques into the renderer.
A nice work around though with Deep that you have a deep front and deep back which is typically in the same location. With a deep expression node you can essentially push the front and back apart and get a nice fuzzy edge on any intersection of surfaces.
Add this deep expression node to your deepRead before you deepMerge. Modify the expression distance to make it look more or less transparent along the intersection.
set cut_paste_input [stack 0]
version 7.0 v8