I'm not sure if this is resolved, but:
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EAGLE has layers (tdocu, bdocu) for drawing that appears in your editing window, but not actually in the produced silkscreen layers.
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one of the advantages of producing gerbers, rather than handing a .BRD file to the PCB manufacturer, is that you can determine exactly what gets put in the silkscreen (usually tPlace, but tNames and tValues maybe, maybe not.) The gerber generation process lets you explicitly select which layers from the .BRD file show up on the actual board layers.
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A PCB manufacturer usually masks the silkscreen layer with the soldermask layer as some part of the process, so that silkscreen does not cover "exposed copper."
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Not all components in all libraries are very careful about tPlace vs tDocu (or vs tNames/tValues, for that matter.) And many don't have very good tPlace pictures (I hate that the default 3mm LED package doesn't have any polarity indication on tPlace, for example.)
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The various ULPs for making sure silkscreen line widths meet minimum requirements (silk-new.ulp and others) work by redrawing the (possibly modified) silkscreen layer objects on yet another layer. If you do this, you can edit THAT layer manually to your hearts content, since the objects are no longer bound to packages.