The thing about meddling with time is that one moment something is real, the next, it’s been erased. Probability becomes just a possibility. Established truth becomes a theoretical falsehood. Like dominoes, as one timeline falls, the others come cascading down around it. You can engineer new timelines, new possibilities, but before long, the distinction between what is, what was, what might be and what never can be becomes blurred.
Out of this grow myths, lies and legends. The Doctor was one such legend, but no one knows whether he truly ever existed. Well, not now they don’t. The Mighty One, ruling the multiverses from the eternal city of Chronopolis, has made sure of that.
Ellie complains that the Valeyard criticises her for carrying weapons unless it suits him. In the proper timeline, the Seventh Doctor's companion Ace frequently raises similar objections. (DW: Remembrance of the Daleks, et al)
The Matrix’s projection of the Sixth Doctor’s missed encounter with Mel is inconsistent with their actual first encounter in PDA: Business Unusual; they didn’t meet at the police station, but the previous day, when the Doctor took her friend Trey Korte back home before realising that he was staying with Mel. However, this story does take place in an alternative timeline, and it is possible that the Valeyard had already changed history in some other way, perhaps erasing Trey or the Nestenes from history.
The Valeyard implies that he’s picked up a weapon which belonged to Jack the Ripper, a probable reference to PDA: Matrix.
Vansell compares the Valeyard to the inchoate form of the Watcher (DW: Logopolis) but claims that it is unprecedented for such a being to achieve independent sentience, implying either that the Time Lords are unaware of the existence of Cho-Je (DW: Planet of the Spiders) or that he was something else entirely.
Vansell refers to the Time Lords once sending the Doctor on an ultimately unsuccessful mission to destroy the Daleks after the Valeyard has altered history by giving the Thals a formula to wipe out the Daleks before their creation. (DW: Genesis of the Daleks)