No, the plate thickness entry is for the movable plate.
When you do the initial auto zero, the tool is zeroed to the movable plate first, using the thickness of the movable plate.
When it travels to the fixed plate, it saves the offset distance of the fixed plate surface relative to Z zero, which is already set.
When you do a tool change, the tool goes to the fixed plate, and uses the saved Z offset distance to set the new tool to Z zero.
Hope this makes sense.