Most of the controlled animals are listed for obvious reasons - venomous, large, dangerous, etc (not that responsible and intelligent people cannot house them correctly and safely - but let's face it - there's some really stupid people out there).
Others are listed because they may pose a threat if released to our native species. I'm not sure if it's true - but I heard the reason some water turtles are illegal to own in Alberta without a grandfathered permit was that the males would kill the native Alberta male turtles and breed with the females. Don't quote me on that though. But, maybe the salamanders are a threat to native ones in some way.
There is one group in the States working with Fish & Wildlife to create a permit system to control animals with very specific care requirements (such as chameleons) as well. Personally, I don't think it will fly - costs, time and the reaction of average hobbyists will be prohibitive.