Unfortunately, Scrivener changes these lower case letters to capitals. Capitals won’t work in my text.
How can I prevent Scrivener from substituting capitals?
No, it won’t, because this isn’t a formatting issue.
You would use Preserve Formatting if, for instance, you had a paragraph set in a different font and didn’t want the Compile command to change it. See Section 15.5.6 in the Scrivener (3) manual for more information.