As a typesetter, I know that the way the footnotes appear in Paratext is not how they print out. Paratext attempts to display the text according to styles, but is very limited in what the output looks like. How it appears in print is handled by other software such as Publishing Assistant, Pathway, or simple Print Draft (Export to PDF).
If you run a print draft (Export to PDF) you should get a better idea of how the footnotes will display.