Something that might help you out is Edit/Paste and Match Style. When you don’t want the original formatting, and want to use what Scrivener is set up to use by default, that’s the ticket.
On your third point, I don’t believe PDF has any such thing as a footnote, in the sense of the feature as Scrivener knows it—a special code. Of course PDF can typeset some text as footnotes, but that is all it is, typesetting. There would be no way for Scrivener to interpret that.