Ah, there's the difference! Some apps allow you to set the "color" of the page. Changing the Opacity to zero makes even the Print PDF come out with a transparent background. I used this
awhile back when Comic Life didn't allow you to copy images to other apps. The iWork apps don't allow you to set the background color, though, so every page that's printed to PDF comes with the white background.
In order to get around this, you Copy from Pages, do Command-N in Preview (the image on the clipboard has no background, so it's transparent) and, to store the image for later use, you can then save as a PDF. If you compare what you get from Print to PDF and Saving a copied image, you'll see that Print to PDF gives the white background (plus the ENTIRE page that you'll need to crop) and passing the image through Preview will yield a PDF image with a transparent background AND already cropped to the size of the image.
In checking what gets pasted into other apps AND what gets saved as a PDF, you retain access to the full smooth scaling of PDF images. As large as you want with no jaggies. The Font question is an interesting one. I've used this for myself (so I have all the right fonts) and have sent PDF images to others that saw what they should see, BUT can't remember if I'd ever included any odd fonts for a test. And, interestingly, there's no color profile listed in Preview for PDF's the same way it's listed for a bitmap. Never noticed that before 🙂