In addition to Fade In's built in File > Create PDF functionality, there may be other ways to create PDF files from the Print dialog, such as OS X's built-in PDF generation capability, PDF virtual "printers" on Windows, and PostScript conversion (or PDF output) on Linux.
For the most part, layout and metrics should be the same between the two, but there are a couple of differences:
1. PDFs created with the built-in Create PDF functionality tend to be noticeably smaller. As an example, one 120-page screenplay results in a 222 KB PDF file using Create PDF, while the same screenplay, output to PDF on OS X using the Print dialog and its Save as PDF option, is 1.5 MB. (This is just one example. File sizes/differences will vary.)
2. Most of the time it won't be an issue, but it's worth noting that the built-in Create PDF functionality has more limited font behavior. The reason for this is that Create PDF uses exactly what fonts are explicitly specified in the document. Sometimes, however, especially when mixing languages/character sets, a particular font may not contain the specific glyph(s) in question. What happens in this case is that the system will generally substitute that glyph from a different font — but Fade In won't actually know it's doing that. So when Fade In goes to output the PDF using Create PDF, it tries to output that character from the font it thinks it's using. When a PDF viewer then goes to display that PDF, it does not find the missing glyph and typically shows a placeholder (like an empty square). "Printing" to PDF, on the other hand, generally uses the system's same font substitution that is used for onscreen display.
(The way to guard against #2 when using Create PDF is to explicitly specify the font. So, for instance, if you're pasting in some Chinese text to an English-language document, also select that Chinese text and specify using Format Fonta font that contains the required Chinese characters.)
Some additional information on this topic is here:
and here:fonts, pdf, unicode