The judge ruled on the case as narrowly as possible to settle the matter before the court (as a prudent judge should do). Because Wong Kim Ark was born after the period in which your proposed definition of “natural born citizen” clearly breaks down (i.e. the period in which persons born as colonial subjects were having children born as United States citizens), the judge was not required to point out the inadequacy of this definition, and exercised judicial restraint in not going out of his way to do so.
I have to be honest, this is a new argument, but it doesn’t make sense. The definition of natural born citizen used by the Supreme Court doesn’t break down. It is a definition in its most pure sense. Any other type of citizenship has to be created and legislated. WKA was born AFTER the 14th amendment. His U.S. citizenship was entirely invented based on a statutory definition of citizenship from English law (it’s not common law, because it wasn’t part of U.S. law) and the 14th amendment. The judge couldn’t use the no doubt definition of natural born citizen for WKA because it didn’t fit.