Transparency for PDFs in Arc

Any transparency layer gets lumped in with the images pdf layer.
ESRI Help
From the advanced pdf features section:

Layers that cause rasterization, such as transparent layers, or layers that use a picture fill symbology consolidate all the layers below them into a single layer with the name Image

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As @Brad already answered - not possible. Transparencies are rasterized in the PDF resulting in HUGE file sizes. Very very poor PDF engine in ArcGIS as you no doubt have realized.

You can turn the transparencies off then export to PDF and open in Illustrator or CorelDRAW and apply transparencies in post processing. Time consuming but possible.

Do not waste your time on exporting to AI. That's even flakier then to PDF.

Other than that you can export from ArcGIS as TIFF (300 or 400 DPI) which produces an enormous file and use Adobe Acrobat Pro 8 or better to convert the TIFF to PDF. Adobe has an awesome rendering engine so it produces a great result. The resulting PDF will be smaller than anything out of ArGIS and much cleaner. It has to be TIFF to PDF Acrobat conversion JPEG to PDF for example will not work the same. Alternatively, you can use Nitro PDF version 7 (might still be in beta) to do the same. It has to be the new version 7 as this is the only version that features the new completely re-written rendering engine. (Don't waste your money on version 6 Pro) The results are comparable or better to that of Acrobat except that Adobe has a better display rendering. In other words - create the PDF in Nitro 7 but use Adobe Reader to view it. Hope this helps.