In Peter David's "One Fateful Knight" in Short Trips: The Quality of Leadership, the Merlin Doctor is the eighth Doctor, straight up, no alternate.
I'm pretty sure the NA presented two other alternatives - a future doctor with red hair and also em.. some other dude who might or might not be an alternative universe doctor who's name escapes me but is in Happy Endings.
Having said that, unlike the River Song situations absolutely nothing is presented on screen but guesswork.