Not quite sure what you're saying here. The pocket, or the end of the fretboard? On mine I just fitted the neck so the end of the fretboard was just back from the edge of the pickup rout. The end of the tenon doesn't butt up against the back of the rout.
With TruOil on the black, it will be more of a very dark brown colour. But you may not get that much differentiation between the wood and the figure and you may just get pretty much all black, unless you use a very weak stain. The mahogany is relatively dark to start with, which doesn't help.
The finish in the photo will have been done with a black tinted lacquer over a stained and sanded maple top, with clear coat on top of that. It really is hard to translate a finish on a light wood to a finish on a very different wood.







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