For years I've "printed to pdf" via InDesign and had no problems with the quality/accuracy of my output. As I've adopted some of the advanced techniques such as knocking objects out with alpha channels and transparency, I've noticed that more and more, my output is flawed. As a result I've reworked my files in Photoshop so that the knockouts and transparency occurs there and is placed into ID as bitmapped artwork.
Recently I was having a problem outputting a file and sort of stumbled upon Export as PDF. When I tried it, my file output perfectly! I'm thrilled to say the least.
What I'm wondering is what's the difference between the two? I'm wondering now why there's even a print to PDF option? If I were Adobe I'd make a clearer distinction between the two and the benefits of both.
Print to PDF is a shortcut for printing to a postcsript file and distilling. Export does not use postscript at all, but instead uses an internal PDF library. Exported PDF supports color management, interactivity, layering, transparency and other advanced features not avaialble in distilled PDF, and is the recommended method for producing PDF from ID.