Did you read anything I wrote? Transparency in vector objects in a PDF are properly limited to those in Illustrator. Some transparency types require RGB PDFs, and some, like Subtract, are properly bitmap transparencies. These types of transparency (bitmap types) are not even available in AI, but are in most decent bitmap editors as they can only be represented in a flattened state. Which is why if you export to a PDF/X format from CD the gray object's appearance is maintained when using Subtract. You can also accomplish the same thing by making a copy of such objects using bitmap transparencies and the underlying objects and creating a bitmap copy at the required resolution for output.
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