I only feel competent to comment on a couple of the subjects you raise. First, it is quite common for only some of the pieces of a set or pair (such as sugar box and lid) to be marked. Second, I have cleaned many pieces including similar brown print, and while I totally agree with Len that much of the overall brown appearance is likely due to actual sugar (or whatever the vessel held at one time or another) infiltration through the glaze, it is not at all uncommon after complete cleaning to still find that the piece has an overall brown tint to the glaze, for whatever reason.
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