For PDF, you can create a separate set of front matter and add a page with the cover. I was never able to get a table of contents to work with PDF, though.
As for the double content header, I have that problem to this day. There are two other threads and 4 years later I still haven’t been able to fix it. There were later threads including one on how to fix it manually after compile using sigil. I have to use sigil to add alt tags for images anyway. I wish scrivener had alt tags and handled accessibility metadata too. It just puts the file name as the image alt tag.