The problem is neither Scrivener’s nor Word’s; both text engines are applying superscript, which is proper in each, but when you when you open your text in Word—or NWP—it is super scripting already superscripted text. You have to turn it off in one of them, and it should be easier in Word, I imagine, just as it is in NWP.
As I said, I haven’t used Word in years, but there must be a way to select all superscripted text and unsuperscript it. Is there no one where you are who really knows their way around Word and can help you do it?
Mark