By their very nature, theories do not prove anything, ever. At best well-performed experiments prove that a theory has accounted for the gathered evidence. So this piece is off to a bad star right at its title. Towards the end it mentions "geological evidence", but does not say what it was. It also mentions a "scan" of Loch Ness, without giving any idea what the scan actually found.
I tried to access Bauer's research article on the Internet, without success. But reports on the article -- in non-scientific publications -- provide a hint to one aspect of Bauer thinking. He might be making an analogy with the seals of Lake Baikal. It has been theorized they are descendants of saltwater seals trapped in an ocean space between two converging continents, then uplifted and the saltwater flushed out (while the seal remained). During the last Ice Age, most of Scotland was depressed below sea level by the massive overlying ice sheet. When the ice melted, the land was flooded by seawater, only to gradually rise above sea level (glacial rebound). During this period saltwater species of various types could have become trapped in lakes that soon enough became fresh water habitats. Many might not have been able to adapt to the new conditions, but some probably could. (Smaller species could chose to use the lakes outlet to access the ocean, but for larger ones that might not have been an option.)
So while these circumstance allow for the possibility of trapped saltwater creature surviving in freshwater lakes (per the Baikal seals), they PROVE nothing about Nessie existence or non-existence.
This THEORY would exclude marine animals from the age of the dinosaurs because they were all extinct eons before the Ice Age. It would also suggest that there are surviving saltwater relatives, since the Ice Age is a relative recent event geologically speaking. Bauer ends up speculating that an unseen creature is related to another unseen creature. On this weak foundation he lays a wager that it is some sort of turtle. It would be delightful if he were right! But I am not holding my breath.
(It occurs to me that the turtle's shell could explain why no dead specimen have washed ashore -- the dead weight of the shell would condemn them to the depths. Has anyone ever dredged up a turtle shell from Loch Ness? Hundreds ought to have accumulated over the millennia. And is there any turtle specie that doesn't lay its eggs on land?)