What people repeatedly mention is the ears being trained. I first though of it as workout or something, but what I think people really mean is audio experiences in using various setups. As you use various gears, etc.., you build a better relative idea of possibilities.
For example, look at Joker's iem thread. After experiencing so many different signature type/styles, you become more grounded to realize particular personal taste, and also the possibilities out there in terms of performance. Like anything experience really does matter. That is really the truth of it.
As an example(not really highly analogous, but proves a point), let's consider medical practitioners over the years. Their practice require empirical evidence, but also there are also grounded in science, but this "science" could be something of tradition that was wrong over many years. Science is sometimes not science. Theories are abstraction of reality, and models don't always fit all circumstances. There are unknowns, and I think people with intelligence acknowledge the unknowns more than think something is a sure thing without much investigations.
Sometimes we run into conflicts, what somebody tells us has scientific grounding, but doesn't coincide with our empiricle experience. We should ask questions, and should not close off possibilities(as long as it's fairly reasonable).