I believe directly in the system settings you can only show/hide an entire menu item in the setting tinymcerte.menubar.
If you want to remove a subitem inside the “Format” menu, you probably have to create an external config file (system setting tinymcerte.external_config) with content like this:
{"menu":{"format":{"title":"Format","items":"bold italic underline"}}}
This shows only the specified items “bold italic underline” in the “Format” menu.
Copy the default items list from the documentation and remove what you don’t want.