Joomla modules can be copied and used in any module position.
JA Templates hard code the menu into a single location.
It would be much better if the template menus were Joomla modules that could be positioned in any module position and could be copied and used in multiple locations.
For example, the mega menu could be used in the main navigation bar at the top of the page and a dropdown css menu could be used in the footer area.
Alternatively, allow the location specific code to be added so that the menu functionality can be reused in other areas.
One last point. While another menu module can be added to the site, it seems like a waste since very good menu functionality is already present in the template.