Is there any way to use a custom FocusTraverser in a plugin?

Is there any way to use a custom FocusTraverser in a plugin? The FocusTraverser is created by the top level component, which is created by the plugin wrapper so there is no way for me to override createKeyboardFocusTraverser?

Not for the top level component, but you can override createFocusTraverser() / createKeyboardFocusTraverser() for the editor or any focus container child to make them return your custom traversers.