I don't see how that follows. My understanding of the Season 6B theory is that yes, they did regenerate Troughton into Pertwee, but only after sending him on missions including "The Two Doctors."
I've always wondered why it was just the Doctor and Jamie in that story. Since no female companion was mentioned, there had to have been a time between Victoria and Zoe when it was just the Doctor and Jamie...
Actually, Victoria is mentioned briefly in The Two Doctors
, as follows:
: We don't usually get to where you say we're going.
The Second Doctor
: I got Victoria to where she wanted to go. Why she wants to learn graphology, I have no idea!"