ID:1108136
 
(See the best response by Jemai1.)
It seems that adding an object with mouse_opacity = 0 and pixel_y offset as an overlay to an object that has mouse_opacity = 2 will cause the hit box for that object to be the size of the object + the amount of pixel_y offset of the overlay.

Other than supplying a dummy hit box for all mobs, what else can I do to keep the overlay purely visual and not increase the hit box size of the atom?
Best response
There's no other way than having them in separate atoms.