It seems non plausible to me that scientists staring at the Hobbit's feet don't entertain at least a fleeting thought the feet are great for water propulsion. Michael phelps had large feet, short legs, and a long powerful torso. The Hobbit is built the same, but with a downward curve of the clavicle, giving the hobbit a streamlined neck to shoulder shape.
Exercise cannot be genetically imparted to the progeny, so it is irrelevant. That large feet incidentally may have helped its survivability is something to look at, but it obviously didn't help the little Ebu Gogo enough.
"Facts are stubborn things; and whatever may be our wishes, our inclinations, or the dictates of our passions, they cannot alter the state of facts and evidence." --John Adams