macstudent,
I understand what you mean about maintaining the transparency in your files as long as possible and I agree with you to a point. It is important to keep the transparency in your layout file (your Quark Xpress file or your Indesign file or even your Illustrator and Photoshop files) that way you can apply changes with relative ease. The whole idea of sending PDF's to a printer is that the PDF's are complete. There shouldn't be any need to change things on PDF's except on some rare occasion. If changes do need to be made, it is usually preferable to make the changes in the original file instead of the PDF. Plus as I mentioned before, printers charge a crazy amount to "adjust" your files.
The link you posted was interesting but you have to take what Adobe says with a grain of salt. Adobe is out to make a profit and so they will make statements that support their software solutions. Just because Adobe says something, doesn't mean that it is always correct in the real world. In an ideal world, every printer would be using the most up to date software and the most recent RIP's and workflows. In reality, many printers are using old RIP's or workflows that can't handle PDF's that contain transparency. In my experience, Adobe only deals in the "ideal Adobe world".
I like Adobe and while I think many of their products are great, they are not infallible. While many people here will tell you how bad Quark Xpress is, Quark XPress is a great product. Without Quark XPress, you wouldn't be using InDesign. You would be using PageMaker. I'm just a little sad that the government allowed Adobe to buy Macromedia. No matter how much I like Adobe's products, I think that the lack of competition will make for a lack of innovation in the their future products.
Again, sorry if I'm necroposting, or whatever the hell you call it, but here's my two pence worth:
Firstly, RIPs that are PDF 1.4-compatible (i.e. can handle PDF with transparency) have been default for what, 10 years now? If some printers or pre-press houses are running RIPs older than that, then really they need to take a look at where they're spending their money.
The fact is such companies that whinge that they can't cope with the files you are sending them, when they are provided with perfect, industry-standard print ready files are basically lazy or greedy and can't be bothered trying to find out 'why' they can't handle the files. The same companies would be working with flat-copy artwork if they could get away with it.
Quark XPress majored in the days when separated PostScript was king (and InDesign didn't exist). It also majored in publishing, i.e. the transmission of the written word in newspapers and magazines. It was abandoned (for Freehand and Illustrator) in other branches of design and pre-press, particularly packaging, years before InDesign even existed.
Where InDesign scores is in the workflow - to go from design, to print ready files, to PDF, to output is seamless and hassle free. Again, I haven't used Quark since V4, and I'm sure it's improved, but they never got a second chance with me.