Recently I drew a simple line on a blank page in Preview. I realized, that if I export the Document via File > Export as PDF, and open the exported Document, I don't have the ability to move around and edit the line. If I alternatively use File > Export and then choose 'Format: PDF' I can edit the exported file later. So this lead me to the question, why there are 2 different PDF Export 'Formats' in Preview. I believe that this might pose a slight security risk, since editable PDF Documents can later be manipulated.
Firstly, PDFs can always be edited, and if you used a decent vector artwork editor (of which Adobe Illustrator, Affinity Designer, Inkscape, and Picta Inc.'s Graphic are examples, and Preview is not), you would be able to move the line from either export method. There is no 'security' to be had.
There are certainly differences between the two types of PDF Export. File > Export As PDF will place your image onto the default paper size. This is most noticeable if you have an image that's not A4 or US Letter. File > Export > Format: PDF will keep the dimensions of the image.
The former type of Export keeps the line data as an annotation, whereas the latter type of export flattens the data as just a 'line' within the PDF.
As to why Preview has such as clumsy interface: only an Apple insider can tell you that. There are many mysteries about why Preview is such a terrible showcase for the brilliant Quartz graphics APIs that lie beneath, and we may never know.