It's true, i don't think he will have the EMS, but who sait that put two sharingans in one eye will give the EMS? It is the opposite, we can suppose something else, for exemple, a new sharingan which give a boost of the ninja's abilities.
Also, you said he can't use both sharingans? If it happens, Naruto have just to use on him a sun mark to give an unlimited chackra or a little more at least.