small survival advantage makes it certain that salamander lives to reproduce? Even healthy organisms get eaten, are the victims of bad luck. And how do we know that the salamander did mate with a similarly endowed (or lack thereof) opposite sex salamander? All conjecture, but if you were building a mathematical model, you would have to factor these considerations in.

I agree about the big jump in mutation--easier to explain in a loss of a body function, just screw up the genes and it doesn't work. Much harder to make this work for the development of a new and improved organ--hence the discredit laid on the hopeful monster.