For those who do not understand the Valeyard, this is a very quick insight into the character and how I see his involvement in the Conquest of Evil Multiverse. So firstly a little background...
The Valeyard was a villain from the BBC television series Doctor Who that appeared as the overarching villain for a whole season against the Sixth Doctor. At first the Valeyard appeared as a prosecutor in the Trial of a Time Lord that sought to have the Doctor executed for his alleged crimes. However his identity was eventually revealed to the surprise of most of those present. The Valeyard was in fact the Doctor himself, or rather an amalgamation of the Doctor's dark side that gained sentience somewhere between the Doctor's twelfth and final regeneration. He was a representation of all the things the Doctor struggled to keep suppressed within himself and had been recruited by another agency to help them bring down the Doctor. In return he was to receive the Doctor's remaining regenerations.
Of course he was defeated by the Doctor although he was not destroyed (how do you completely destroy your own dark side without destroying yourself in the process?). He returned at a later time in the BBC Doctor Who books where he was supposedly eliminated.
Now my view of this is that the Doctor never truly defeated the Valeyard. All he managed to do was overcome him as most people do. However with Doctor Who there is always the problem of regeneration. The Doctor's personality changes from one incarnation to the next in addition to changing as he ages. What does that mean? Well the Sixth Doctor was much different than his predecessor. There was a harshness and an underlying sense of anger and borderline insanity that was reflected by the Valeyard. The Seventh Doctor was also darker than most but was also a manipulator, going so far as to prematurely end his previous self's existence just to exist. And when the Valeyard appeared in the BBC book, you could see how he had become more manipulative than before.
This got me to thinking that perhaps the Valeyard was more than just the Doctor's dark side. Maybe he was a snapshot of how the Doctor would be as a villain taken from the moment he encountered his previous self. I've long believed the A Season to Remember in Power Rangers Zeo was an example of how future events depicted in the show are a snapshot future based on how events are at the time of viewing. Hence Kat and Tommy could be together in the future because they were at that the moment those events took place, however an earlier season might have revealed Tommy with Kimberly and a later season something else.
The same holds true with the Valeyard as far as Conquest of Evil is concerned. If the Valeyard had encountered the First Doctor he would have been solely the First Doctor's negative. And of course while that would make him more dangerous for the darker Doctors.