Every time I save a webpage in Safari as a PDF to a Scrivener project Safari crashes.
It is not that bad because a) the PDF gets properly sent to Scrivener before the crash and b) when you restart Safari each of its closed tabs or windows automatically gets re-opened. Still annoying.
Maybe this is part of the known general PDF problem in macOS Sierra.
You could try recreating the “Save as PDF” alias to see if there is a problem with that. You’ll find these located in the “~/Library/PDF Services” folder; just remove the existing “Save PDF to Scrivener” alias and then restart the software letting it recreate the alias.
Beyond that, this sounds to me more like a problem with Safari. As you can probably guess from the mechanics of how these exist, there is no difference at all between dragging a PDF onto Scrivener’s icon in the Dock, to an alias on your Desktop, or the icon in Applications folder. The only special thing that is going on here is macOS adding a list of “Save PDF to BlahBlah” entries in that universal print dialogue.