Okay, so this is me just working out some headcanon fan theory stuff, but…
(You might want to refer to this post to keep track of what the hell I’m talking about here).
Klein’s Story established that the Seventh Doctor has regenerated into the McGann!Doctor on two separate occasions. This would suggest that if a regeneration cycle is left to play out naturally then it’s inevitable that a particular “face” will follow on from each incarnation no matter the circumstances of that regeneration. So, McCoy!Doctor will always regenerate into McGann!Doctor, no matter when he regenerates.
Now, it is safe…logical, maybe…to assume that Eight’s regeneration into the War Doctor is an exception to this, as it was a controlled regeneration brought on by the potion given to him by the Sisterhood of Karn. He did not regenerate normally, but chose the form he regenerated into (ie. a warrior).
Now, we also have two alternate timelines in which it makes sense to assume that this never happened. In both the Shalka timeline and the Curse of Fatal Death timeline we can assume that Eight’s regeneration happened normally, without the involvement of the Sisterhood of Karn. Now, it’s interesting then that Shalka!Doctor and the Alternate Tenth Doctor from Curse of Fatal Death both wear the same face, that of Richard E Grant.
It has always been assumed that Eight regenerated into Shalka!Doctor, but if I recall correctly there’s nothing in either Scream of the Shalka or The Feast of the Stone that explicitly states this. Also, Shalka!Doctor has, indeed, often been referred to as an alternate form of Eccleston!Doctor, who is technically the same incarnation as the Alternate Tenth Doctor from Curse of Fatal Death.
So, here’s my theory/head canon – Shalka!Doctor and the Alternate Tenth Doctor from Curse of Fatal Death wear the same face because they are the same incarnation of The Doctor in different timelines, but both timelines follow the natural progression of regenerations without alteration by the Sisterhood of Karn. Therefore the Curse of Fatal Death shows us how The Doctor would have regenerated if he had never taken the potion in Night of the Doctor. We must assume, then, that Eight did not regenerate into Shalka!Doctor in the Shalka timeline, but regenerated into Atkinson!Doctor who then regenerated into Shalka!Doctor.
Thus we neatly account for two different incarnations of The Doctor having the same face – they weren’t different incarnations at all. Also, we must assume that the potion given to him by the Sisterhood of Karn had the knock on effect of making all his further regenerations take a different form than they would have if his cycle had been allowed to progress naturally. So, ultimately, if it wasn’t for the Time War then Matt Smith would have been Joanna Lumley.
I have no doubt that there’s plenty of EU stuff that flatly contradicts this theory, but right now it works for me.