Use the Split feature after you combine the bodies
1) Why do you need to combine them? They are touching, which should be good enough.
2) You aren't going to be able to do what you want, as the "Do not Merge" area of your picture will result in a zero thickness geometry area.
3) one alternative is to drop the weld beads slightly into the surface of the parts. But you still won't be able to merge unless you put some sort of physical gap between the two plates.