Easy to do, and I think it's quite understandable too. If you create a page layout in Illustrator and you leave it to your printer to import it into a picture box in Quark, it may not be positioned correctly. Quark places the top left corner of the Illustrator objects in the top left corner of the picture box, not necessarily the top left corner of the Illustrator page.
If you have elements beginning too far in or off of the page, it takes a little more effort on the part of your printer to correct it in Quark (which is probably where the rest of the publication is being put together). If they've got dozens of ads to place with deadlines looming, then of course they'd prefer if you positioned it yourself. A simple copy & paste on their part is far less error prone for them, and having seen the way some people put ads together in Illustrator, I couldn't really blame any printer for covering themselves!