Which is why myself and other prepress haven't moved to PDF until we can get something like the Adobe PDF Print Engine, where transparency is not flattened, and a PDF can go through at the PDF's native version, with full "live" (unflattened) transparency, only changing version when a layer is added for traps (requires higher version than PDF 1.4). This would allow the same edit-ability as we have with native files (Adobe, Quark). You could edit type using the PDF's fully embedded fonts, edit transparency/opacity/blend modes, edit fully embedded images in Photoshop. However, as we know, Adobe can handle exporting this type of PDF, but Quark can not. Until then, I might as well stay with native files. When I do get a workflow like what I'm describing, then layering shouldn't be a problem IMO. Heck, even now layering is only a problem if I need to edit the PDF/X I receive. Otherwise, it doesn't affect me. I rip and run these jobs in Nexus and don't have a problem with "soft" 300 dpi edges of some type (especially when I look at the print - it's not that noticeable).
> Note that for QuarkXPress (for which I obviously do not claim exertise), PDF export yields an internal process in which all transparency is flattened, PostScript is generated, and PDF is created from that PostScript by a process other thanvia Distiller. You probably can guess what I think of that!
> - Dov
Distiller makes a better pdf than Quark. That I can understand. What I don't get, is how Distiller can make a better PDF then Quark when supplied with a QUARK PostScript?!?! If Quark can make a good PostScript, then why can't it convert that PostScript to PDF better than Distiller. Doesn't Quark have the advantage of full control over the process, where as Distiller is forced to do what it can with what Quark gives it?
Put it like this. Quark is only really making the PostScript either way. I let Adobe make the PDF from the PostScript, and Quark let's Jaws PDF Creator make the PDF from the PostScript. It's obvious Quark doesn't know how to make a PDF, or how to import one with transparencies and print it either.
Bottom line: Quark and PDF are not friends in any capacity if you want reliability.
I'm a bit late in chiming in on this but Callas Software has pdfAutoOptimizer for Windows that will allow you to drive Acrobat 7 Pro's PDF Optimizer feature that will allow you to flatten transparency in all your PDF's. And I'm assuming that when you create the PDF's that you're taking care of the flattening on your end. But the PDF's coming into you are a different subject. And that's where pdfAutoOptimizer comes in handy.
If you'd like more information please feel free to let me know.