Typically you mark the good side so that you can reference everything with out having to think the reverse. Very commonly solid wood is attached to the edge of plywood and unless both are perfectly the same thickness you can throw off the height location of the slot being cut. If one board is thicker than the other and the good side is up your slots will be off the same distance as the difference in thicknesses. If you let the fence rest on the material rather than having the plate joiner base setting on the bench the upper surfaces are correctly referenced.
Add to that if you are using the bench surface to reference the plate joiner to the material, debris can often raise the plate joiner up and throw off the slot locations.
Add to that if the material is slightly warped and bows and you use the bench surface to reference the plate joiner it will cut the slot lower down from the top surface of the material. The plate joiner should always be referenced off of its fence for consistent cuts.