I was asked how to format footnotes when using Scrivener, which led me to the question how to preserve formatting styles when compiling Scrivener into Microsoft Word documents.
While Scrivener is the best writing software I have ever worked with (and still work with), it is not made to format texts. The focus is on writing. Personally, I highly recommend using Scrivener to create the text, edit it, put out draft after draft until the text is “finished”. And then compile the text and use another program to create a nicely formatted text.
While I used InDesign for my PhD thesis, many users will probably want to use Microsoft Word or a similar program. Personal hatred aside, Word does have a few strengths. And if you use a lot of footnotes and want more control over them, you might want to use it for the final version. Not to mention that many people still use it, so if you want to give it to your supervisor, you probably have to.