Difference between Export PDF and Print to PDF in Safari
"Save as PDF" is essentially a digital copy of what you get if you were to print a specific page from Safari. This includes extra headers/footers that include the date, webpage, number of pages, web address, etc.

"Export as PDF" is a simple snapshot of the page as is and does not include all of those extra details. 

From the few pages I've compared the differences with these two options, Export as PDF tends to retain more of the formatting details whereas the Save as PDF option can cause the page to look slightly different.