His concern is if we see patterns (which we do) and this makes it easier to read music, what if the music is constructed out of unfamiliar or meaningless strings of notes. He finds it hard to imagine what kind of level of focus we should have in order to read the words and the music without patterns - literally. He has a good analogy with a spy who would need to remember multi-digit or multi-letter code.
That's a great question and very accurate description of what happens when we read music or words. That's exactly right - what is valid in the language, is very often valid in the musical language as well.
We really do see patterns - arpeggios, cadences, familiar chord progressions, even our fingers remember their position on the keyboard. This means that if all things being equal, an organist who is better at music theory, not only is able to understand musical composition better and on a deeper level but also he or she can sight-read better too.
But if the music is hardly predictable or seemingly meaningless, you will not see patterns so easily. Just like in the code which needs to be deciphered.
Do you like deciphering musical language?