In the header/footer section of the Page Settings tab in “Compile” I can only choose what to display and the font, but nothing about the position (for example, i’d like the page number in the footer to stay a bit higher) nor anything a bit fancier like a line to separate the header from the page.
Scrivener only supports basic headers and footers - they appear halfway down the margin and you can choose what is on the left, middle and right of the header and footer. They do everything that’s needed for the vast majority of formats, but if you need something more complicated or specific, just export to your preferred word processor or dedicated layout program and handle it there.