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...
It seems to me that there are four causes so far:
The interesting one is poison. Obviously, regeneration must purge the body of the poison, otherwise he'd keep dying until he ran out of regenerations. So, if he were to die of a fatal, communicable, disease, the same would likely occur. Or would the new body simply be immune to the poison or disease? This could lead to an interesting situation where the Doctor contracts a disease, regenerates, and is subsequently a source of antibodies.
Another interesting scenario would be if he died of cancer (can Time Lords have cancer?). How would the regeneration effect the cancer cells? All sorts of possibilities present themselves here, the most obvious being a sort of evil twin, a personification of the cancer.
Suppose he died of decapitation or a severe head injury? This is a specific case of trauma, but one still has to wonder how it would effect the next regeneration. It would depend upon the specifics of the regeneration process, of course, but it's possible that the next Doctor could be retarded or at least amnesiac.
This is an interesting train of thought.
Yeah, I can just imagine that not having a head might lead to amnesia...
^That's true I guess, though it doesn't explain why the Doctor doesn't keep trying new bodies till he gets a ginger one
Except that Romana was better at a lot of things than the Doctor was. Some Time Lords may have enough self-control or training of the right kind to be able to guide their regenerations, whereas for the Doctor it's pure trial and error. Maybe that's because he fled Gallifrey before he'd ever regenerated, and so he never had occasion to learn. (Although it's generally assumed, given Romana's young age, that she'd never regenerated before either. So that wouldn't really explain it.)
It was made clear in The Ribos Operation that Romana is in the top-whatever percent of her class. Her Academy grades are higher than the Doctor's, so I just took that to mean she knew the biology and psychology of regeneration better than the Doctor did.