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I talked to an instructor at colege and his explanation was that unless the joins are extremely tight, capilary action draws the varnes or stain into the end grain of the joints, and end grain stains darker than the face. Sanding won't do much as the stain is drawn into the join. His suggests kerfing the board but just stoping short of the top, as the moulding does not have as much wood as the rest of the board it shoud bend, or you could kerf the board with a mitre saw and the moulding part with a thin bladed hand saw, maybe also soaking it.

But I first want to try using oak veneer on the flat part of the board first before I try the above, any comments?