Your submitted PDF might include a coloured area with a semi-transparent layer over the top. Of course the actual printing device isn’t going to do semi-transparent overprinting; it just prints a single image. This means that software somewhere needs to convert multiple layers into a single layer, modifying colours as necessary to (hopefully) achieve the intended effect. This is known as “flattening” a PDF document and doing it correctly, in the face of the various colour spaces used for documents and printers, is not simple.
The digital proof PDF you receive will have been flattened and probably processed in other ways. A CMYK printer has four ink colours so you might think it can print 400% coverage, but often they’re limited to 240%; your PDF might need to be modified to suit. You should check carefully to ensure that it looks the way you want.
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