If the door is opaque it doesn't matter. The surface dimensions are not changed from that shown when calculation of the surface areas for heat transfer to occur. This is good because you know what the surface area of each construction is because you have to explicitly model it. The floor thickness doesn't impact the wall area when heat transfer is calculated.Â
If the door is a window than I reference the top of the window to the top of the thermal block but I have to admit I do this because it is the right way to do it in DesignBuilder and I'm not certain if the convention is exactly correct for OpenStudio. The only bits of E+ that would be impacted would be the daylighting as the heat transfer etc should be the same (depends on which daylight model is selected I think).
Does anyone define these items differently? Why?