Well, the Doctor did say in Rise of the Cybermen that travel between universes used to be a thing back when the Time Lords were around.
Haven't dug the DVD out for a while, but I did think it was mentioned in the extras for Inferno that The Doctor was indeed the Leader. Given the fact that Alternative Liz, Benton and the Brig never recognised him, it's possible it was another incarnation (assuming the regenerations would have been the same). Indeed the Time Lords could well exist in the alternative universe, but there's nothing to say that The Doctor would ever be encountered. The Universe is a big place, and assuming The Doctor ever fled Gallifrey at all, there's always the possibility that he landed on, and gained an affection for, another race out there in the cosmos. However, the catalyst that led to the formation of Torchwood in our universe was The Doctor, and Pete's World did have their own version, so who knows?
It's mentioned that the NA Revelation says the Leader's face was one offered to the Doctor at his trial, and therefore he was the mirror-Doctor. However, the photo of Jack Kine used as the Leader looks nothing like any of the ink drawings shown in The War Games, so clearly the Doctor was delusional when he thought that.
That's hardly conclusive. Perhaps in the Inferno universe, The Doctor regeneration by different means, or simply had a different selection of faces to chose from.
Well, it's our universe's Doctor, so if the Infernoverse's one was dealt with differently or was offered a different set, he wouldn't recognise the face from this universe's set...