OK, the PDF/x1-a (PDF 1.3) specification from the the ISO is not allowed to have transparency or color management. Check in with your printer and see if they can handle a PDF/x4 (PDF1.6). This allows for transparency and color management. You say it's a digital job, so there should not be a problem. The fine white lines you see in the PDF are flattening artifacts. They will freak you out on screen, but they do not print. You can see how the flattening is going to take place using the Flattener Preview from Window > Object and Layout > Flattener Preview. The Separations Preview window has nothing to do with flattening. You can read more about it here. Flatten transparent artwork in Adobe InDesign HTH
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