PDF watermarking may use many of the subtleties of the physical world. If you think of a banknote, some watermarks seem inside the paper whilst others are on top. You can get something similar with PDF watermarks.
Think of the information being printed as if it were in layers, rather like a sandwich. The content sits in the middle, and the PDF watermarking can be over, or under the content, or both. Also the PDF watermark can be set to be lighter or darker than the content. In this way PDF watermarking is able to ‘blend’ with the content so that it has a more seamless presentation. This can help the PDF watermark to be less visually distracting – unless, of course, you want it to be very much in your face.
So applying PDF watermarking takes a certain amount of discipline and artistic judgement, it is not necessarily a mechanical process of having a ‘bog standard’ graphic and/or text and applying it to every document that goes out.