The only reason why its called an Eternal Mangekyo Sharingan is because he'll never go blind with it. Its still a Sharingan though and so keeping it at EMS stage all the time must be extra draining on his body. There's nothing saying he can't turn it on and off at will. So like with the normal MS, Madara should be able to go back in forth between his normal eyes, 3-tomoe sharingan, and EMS with no issues.
Anyway, my biggest issue with Danzou = Madara is, how could Itachi identify a masked man as the late, great, invincible Uchiha Madara when no one else noticed him but standing face to face with Danzou (assuming he's Madara too) doesn't tip him off?