Ha! Thanks very much, hadn't thought about doing that test. As always, something interesting came up…
I got the same mismatch when I printed this two-page document with or without crop marks – same thing when I printed both from an exported PDF and directly from Indesign (thinking, foolishly, something might be “messing up” at the export stage). Same milimeter or so. In fact, I got the same mismatch when I printed the first page with the rectangle twice and placed the two pages on top of each other.
The interesting part came when I decided to set up another two-page document with two rectangles without the Facing pages property… No mismatch. I'm baffled beyond belief. Does this happen because of the Indesign setup then? If so, what then – isn't this the standard practice of setting up an Indesign document for print, when it's a book that is – with facing pages? Has anyone had mismatching problems when printing a PDF/Indesign file prepared in such a way?
The only comforting bit of this whole thing is that when I align the crop marks manually, when raised up against a light source to match through the paper, there's no mismatch on the rest of the content – illustrations or rectangles…