My take was that he was a recreation of the Valeyard, but it was also his origin in the post-Time War timeline. So I would say that the original Valeyard from the pre-Time War universe is dead and defeated as per The Last Adventure but now this new version exists trapped within The Time War. It’s made pretty clear that the only reason he’s such a nice chap is because of his amnesia and if he left the time loop he’d just revert into the regular old Valeyard.
Ties back rather nicely with the Doctor's assertion in
The Five Doctors: "A man is the sum of his memories, a Time Lord even more so." Remove all that makes the Valeyard who he is and, well, he's the negative space left after the fact. He's the Doctor.
I've given this some thought, so I'll put aside the timeline itself for the moment and just talk about the different interpretations of the Valeyard we've seen (circa 2020):
~
The Trial!Valeyard - The original who we first met during
Trial of a Time Lord. The Wickham to the Doctor's Darcy. His time seems fairly straightforward, although, I remember someone (John Dorney?) suggesting that for
The Last Adventure, the Valeyard's timeline is actually happening backwards respective to the Doctor. In that scenario, he's first defeated in
The Brink of Death and biding his time for another return. The Valeyard might have been first found, incapable of speech and half-mad, on Etarho by scavengers as per his
Trial of the Valeyard tale. It's an unreliable narrator so how much is true is open for debate.
(
In publication order: The Trial of a Time Lord, Mission: Impractical, Time's Champion, Trial of the Valeyard, The Last Adventure, Every Dark Thought)
The Rites!Valeyard - A personification of existential anxiety. The Doctor's own imaginings of the Valeyard, made manifest by the quantum mnemonics of
Millennial Rites, temporarily subsuming the Sixth Doctor beneath an entirely new personality. He's banished by the traveller through force of will, but eventually, he's made manifest again in
Head Games by another external agency (in this case, the Land of Fiction). I'd say he's how the Doctor imagines the Valeyard to be, but with Time Lords it seems a lot more complicated than that. He's potential.
(
In publication order: Millennial Rites, Head Games)
The Ripper - A Valeyard who has thrown off the title in favour of Ripper. The product of his experiments with the Dark Matrix, he's probably the closest that the Valeyard has come to a unilateral success. He leads a coven of Doctors scavenged from a timeline in which he succumbed to his darker impulses. One of them is a Fifth Doctor who let Peri die. Another is a First Doctor who murdered his way off Gallifrey. He's a lot more vicious here. Notably, the Ripper doesn't regenerate, he dies instead. His final words to the Doctor feel rather conclusive: (
Matrix)
The War!Valeyard - His Time War variant who lost his memory and ironically became the most Doctorish of his iterations.
(
Fugitive in Time, The War Valeyard)
~
Now, how do we put all this together? Well, more or less as it fell above, albeit with a few pernickety tweaks. The Doctor and the Valeyard are both two halves of the same coin. Both exist as the other's shadow aspect, the negative impulses that they suppress in order to be who they are. Neither wants to acknowledge that they share something in common. The Valeyard especially as he wants to exist in a life on his own terms. Be his own person. As a result, when the Doctor does finally acknowledge that the Valeyard is a part of him (
Time's Champion or
Matrix, chronicler's choice), he wins that struggle. His darker half, however, continues to be pulled down further and further -- at least, in his eyes -- by the "contamination" of his other self.
I really like the progression from
Matrix to
The War Valeyard. In the first instance, the Valeyard/Ripper's not only determined, but desperate to prove his own existence. It obsesses him to no end. He's given up trying to exist separate from the Doctor and instead confronts him directly. Reclaiming his other half's life as his own. Rewriting it. Revising it. When the Ripper dies, it's a final release of sorts and his body is collected to be taken... elsewhere. My interpretation is that
The War Valeyard is the conclusion of that struggle. There's a certain poetry to it. He spent so long in denial, trying not to be the Doctor, that all that repression came and swallowed him whole.
When faced with the decision to be the Valeyard or the Doctor -- he chose the Doctor. His shadow. Fittingly, the opposite of what his other self chose.