Not sure that I would thicken the decal very much or at all. Remember, in HO scale the patch plate of 1/4 inch thickness would only be 0.00275 of a real inch when reduced to scale size.
It has been along time since I have actually seen a real steam era box car but I would believe that some of the contrast of the offset plate is because of weathering that has accumulated atop the overlap.
One question from a modeler that must confess has not paid much attention to the PRR… when did the X31s begin to have the patch plating applied? Also was this a class wide program?